Python preparation.PDBComplex类代码示例

 def test_1bju(self):
     """Binding of ACPU to bovine tripsin(1bju)
     Reference:  Presnell et al. Oxyanion-Mediated Inhibition of Serine Proteases.(1998)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1bju.pdb')
     bsid = 'GP6:A:910'
     for ligand in tmpmol.ligands:
         if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     #@todo Publication show hydrogen bond interactions for Gly219
     # Hydrogen bonds to Ser190, Ser195, Gly219 and Asp189
     hbonds = {hbond.resnr for hbond in s.hbonds_pdon+s.hbonds_ldon}
     self.assertTrue({189, 190, 195}.issubset(hbonds))
     # Water bridges to Ser190 and Val227
     # Water bridge to 190 not detected due to prioritization
     waterbridges = {wb.resnr for wb in s.water_bridges}
     self.assertTrue({227}.issubset(waterbridges))
     # hydrophobic interaction of Leu99
     hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
     self.assertTrue({99}.issubset(hydrophobics))
     # pi-stacking interaction with His57
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({57}.issubset(pistackres))

 def test_3r0t(self):
     """Binding of protein kinase CK2 alpha subunit in with the inhibitor CX-5279 (3r0t)
     Reference:  Battistutta et al. Unprecedented selectivity and structural determinants of a new class of protein
     kinase CK2 inhibitors in clinical trials for the treatment of cancer (2011).
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/3r0t.pdb')
     bsid = 'FU9:A:338'
     for ligand in tmpmol.ligands:
         if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     # Hydrogen bonds to Val116
     hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
     self.assertTrue({116}.issubset(hbonds))
     # Water bridges to Lys68 and Trp176
     waterbridges = {wb.resnr for wb in s.water_bridges}
     self.assertTrue({68, 176}.issubset(waterbridges))
     # Saltbridge to Ly68
     saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
     self.assertTrue({68}.issubset(saltb))
     # hydrophobic interaction of Val66, Phe113 and Ile174
     hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
     self.assertTrue({66, 113, 174}.issubset(hydrophobics))
     # pi-stacking interaction with His160
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({160}.issubset(pistackres))

 def test_1HPX(self):
     """
     HIV-1 Protease complexes with the inhibitor KNI-272
     Reference: Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog
     containing allophenylnorstatine.
     Note that the residue numbering is different in the publication and the PDB structure.
     For residues in the B chain, the offset is -100 (e.g. Ile 50B in the PDB structure is Ile 150 in the paper).
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1hpx.pdb')
     bsid = 'KNI:B:900'
     for ligand in tmpmol.ligands:
         if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     # Hydrophobic contacts to Val82, Ile84, Ile150 as part of flap (S1, S1' sites)
     hydroph = {str(hyd.resnr)+hyd.reschain for hyd in s.all_hydrophobic_contacts}
     self.assertTrue({'82A', '84A', '50B'}.issubset(hydroph))
     # Hydrogen bonds
     hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_ldon+s.hbonds_pdon}
     # Additional hbond to 25B not detected (low angle?)
     self.assertTrue({'29B', '48B', '27B', '25A'}.issubset(hbonds))
     # Water bridges
     waterbridges = {str(wb.resnr)+wb.reschain for wb in s.water_bridges}
     # Waterbridge with Gly27 is detected instead of Ala28/Asp29
     self.assertTrue({'50A', '50B', '29A'}.issubset(waterbridges))
     print(waterbridges)

    def test_3pxf(self):
        """Binding of ANS to CDK2 (3pxf)
        Reference: Betzi et al. Discovery of a potential allosteric ligand binding site in CDK2 (2012)
        """
        tmpmol = PDBComplex()
        tmpmol.load_pdb('./pdb/3pxf.pdb')
        bsids = ['2AN:A:305', '2AN:A:304']
        for ligand in tmpmol.ligands:
            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) in bsids:
                tmpmol.characterize_complex(ligand)

        s = tmpmol.interaction_sets[bsids[0]]  # 2AN:A:305
        # Hydrogen bonding of Asp145 and Phe146
        hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
        self.assertTrue({145, 146}.issubset(hbonds))
        # Salt bridge by Lys33 to sulfonate group
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({33}.issubset(saltb))
        # Naphtalene positioned between Leu55 and Lys56, indicating hydrophobic interactions
        hydroph = {hydroph.resnr for hydroph in s.hydrophobic_contacts}
        self.assertTrue({55, 56}.issubset(hydroph))

        s = tmpmol.interaction_sets[bsids[1]]  # 2AN:A:304
        # Salt bridges to sulfonate group by Lys56 and His71
        saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
        self.assertTrue({56, 71}.issubset(saltb))
        # Napthalene with hydrophobic interactions to Ile52 and Leu76
        hydroph = {hydroph.resnr for hydroph in s.hydrophobic_contacts}
        self.assertTrue({52, 76}.issubset(hydroph))

 def test_ids(self):
     """Test if the atom IDs are correctly mapped from internal to original PDB."""
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1vsn.pdb')
     bsid = 'NFT:A:283'
     for ligand in tmpmol.ligands:
         if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     for contact in s.hydrophobic_contacts:
         if contact.restype == 'ALA' and contact.resnr == 133:
             self.assertEqual(contact.ligatom_orig_idx, 1636)
             self.assertEqual(contact.bsatom_orig_idx, 994)
         if contact.restype == 'ASP' and contact.resnr == 61:
             self.assertEqual(contact.ligatom_orig_idx, 1639)
             self.assertEqual(contact.bsatom_orig_idx, 448)
     for contact in s.hbonds_ldon + s.hbonds_pdon:
         if contact.restype == 'GLN' and contact.resnr == 19:
             self.assertEqual(contact.a_orig_idx, 1649)
             self.assertEqual(contact.d_orig_idx, 153)
         if contact.restype == 'CYS' and contact.resnr == 25:
             self.assertEqual(contact.a_orig_idx, 1649)
             self.assertEqual(contact.d_orig_idx, 183)
         if contact.restype == 'ASN' and contact.resnr == 158:
             self.assertEqual(contact.d_orig_idx, 1629)
             self.assertEqual(contact.a_orig_idx, 1199)
     for contact in s.halogen_bonds:
         if contact.restype == 'TYR' and contact.resnr == 67:
             self.assertEqual(contact.don.x_orig_idx, 1627)
             self.assertEqual(contact.acc.o_orig_idx, 485)
         if contact.restype == 'LEU' and contact.resnr == 157:
             self.assertEqual(contact.don.x_orig_idx, 1628)
             self.assertEqual(contact.acc.o_orig_idx, 1191)

 def test_1n7g(self):
     """Binding of NADPH to MURI from Arabidopsis thaliana (1n7g)
     Reference:  Mulichak et al. Structure of the MUR1 GDP-mannose 4, 6-dehydratase from Arabidopsis thaliana:
     implications for ligand binding and specificity(2002)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1n7g.pdb')
     s = tmpmol.interaction_sets['NDP-A-701']
     # Hydrogen bonds to Thr37, Gly38, Gln39, Asp40,  Arg60, Leu92, Asp91, Ser63, Leu92, Ala115, Ser117,
     # Tyr128, Tyr185, Lys189, His215 and Arg220
     # Publication give the Prediction for Asp91 as hydrogen bond, when this contains two acceptor atoms.
     hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
     # #@todo Hbond to 128 not detected
     self.assertTrue({37, 38, 39, 40, 92, 63, 92, 115, 117, 185, 189, 215, 220}.issubset(hbonds))
     # Water bridges to Gly35, Thr37, Gly38, Asp40, Arg60, Arg61, Ser63, Asn66, Ser117, Tyr128, Lys189, Arg220
     waterbridges = {wb.resnr for wb in s.water_bridges}
     # Hydrogen bonds to 35, 37, 38, 40, 63, 117, 128, 189, 220 not detected due to prioritization
     self.assertTrue({60, 66, 61}.issubset(waterbridges))
     # Saltbridge to arg60, Arg61, Arg69 and Arg220
     saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
     # #@todo Additional saltbridges report to 69 and 200 (with large distances)
     self.assertTrue({60, 61}.issubset(saltb))
     # Cation-pi interactions with Arg60
     picat = {pication.resnr for pication in s.pication_laro}
     self.assertEqual({60}, picat)

 def test_1aku(self):
     """Binding of Flavin mononucleotido with D.Vulgaris(1aku)
     Reference:  McCarthy et al. Crystallographic Investigation of the Role of Aspartate 95 in the Modulation of the
     Redox Potentials of DesulfoVibrio Vulgaris Flavodoxin.(2002)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1aku.pdb')
     bsid = 'FMN:A:150'
     for ligand in tmpmol.ligands:
         if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     # Hydrogen bonds to Tht59 and Trp60
     hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
     self.assertTrue({59, 60}.issubset(hbonds))
     # Water bridges to Asp63 and Tyr100
     waterbridges = {wb.resnr for wb in s.water_bridges}
     # Water bridge to Tyr100 not detected due to prioritization
     self.assertTrue({63}.issubset(waterbridges))
     # hydrophobic interaction of Trp60
     hydrophobics = {hydrophobic.resnr for hydrophobic in s.all_hydrophobic_contacts}
     self.assertTrue({60}.issubset(hydrophobics))
     # pi-stacking interaction with Tyr98
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({98}.issubset(pistackres))

 def test_2iuz(self):
     """Binding of C2-dicaffeine to Aspergilius fumigates(2iuz)
     Reference:  Schüttelkopf et al. Screening-based discovery and structural dissection of a novel family 18 chitinase
     inhibitor.(2006)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb("./pdb/2iuz.pdb")
     bsid = "D1H:A:1440"
     for ligand in tmpmol.ligands:
         if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
             tmpmol.characterize_complex(ligand)
     s = tmpmol.interaction_sets[bsid]
     # Hydrogen bonds to Trp137, Trp184
     hbonds = {
         hbond.resnr for hbond in s.hbonds_pdon
     }  # res nr 52 mentioned in alternative conformation, not considered
     self.assertTrue({137, 384}.issubset(hbonds))
     # Water bridges to Trp137
     waterbridges = {
         wb.resnr for wb in s.water_bridges
     }  # res nr 52 mentioned in alternative conformation not considered
     self.assertTrue({137}.issubset(waterbridges))
     # pi-stacking interaction with Trp384, Trp137 and Trp52
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({52, 137, 384}.issubset(pistackres))

 def test_dna_rna(self):
     """Test if DNA and RNA is correctly processed as ligands"""
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1tf6.pdb')
     # DNA ligand four times consisting of 31 parts (composite)
     self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4)
     for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]:
         if len(ligset) == 4:
             # DNA only contains four bases
             self.assertEqual(ligset, set(['DG', 'DC', 'DA', 'DT']))

 def test_1p5e(self):
     """Binding of TBS to CDK2(1p5e)
     Reference: De Moliner et al. Alternative binding modes of an inhibitor to two different kinases. (2003)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1p5e.pdb')
     s = tmpmol.interaction_sets['TBS-A-301']
     # Halogen Bonding of Ile10 and Leu83
     halogens = {halogen.resnr for halogen in s.halogen_bonds}
     self.assertTrue({10, 83}.issubset(halogens))

 def test_1vsn(self):
     """Binding of NFT to Cathepsin K (1vsn)
     Reference: Li et al. Identification of a potent and selective non-basic cathepsin K inhibitor. (2006)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1vsn.pdb')
     s = tmpmol.interaction_sets['NFT-A-283']
     # Hydrogen bonding to Gly66
     hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
     self.assertTrue({66}.issubset(hbonds))

 def test_1acj(self):
     """Binding of Tacrine (THA) to active-site gorge of acetylcholinesterase (1acj)
     Reference: Harel et al. Quaternary ligand binding to aromatic residues in the active-site gorge of
     acetylcholinesterase.. (1993)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/1acj.pdb')
     s = tmpmol.interaction_sets['THA-A-999']
     # pi-stacking interaction with Phe330 and Trp84
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({330, 84}.issubset(pistackres))

 def test_3OG7(self):
     """Inhibitor PLX4032 binding to B-RAF(V600E) (3og7)
     Reference: Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant
     melanoma (2010)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/3og7.pdb')
     s = tmpmol.interaction_sets['032-A-1']
     # Hydrogen bonds
     hbonds = {str(hbond.resnr)+hbond.reschain for hbond in s.hbonds_pdon+s.hbonds_ldon}
     self.assertTrue({'594A', '530A'}.issubset(hbonds))

 def test_4alw(self):
     """Binding of benzofuropyrimidinones compound 3 to PIM-1 (4alw)
     Reference:  Tsuhako et al. The design, synthesis, and biological evaluation of PIM kinase inhibitors.(2012)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/4alw.pdb')
     s = tmpmol.interaction_sets['HY7-A-1308']
     # Hydrogen bonds to Asp186
     hbonds = {hbond.resnr for hbond in s.hbonds_pdon}
     self.assertTrue({186}.issubset(hbonds))
     # Saltbridge to A186 and Glu171
     saltb = {saltbridge.resnr for saltbridge in s.saltbridge_pneg}
     self.assertTrue({186, 171}.issubset(saltb))

 def test_3thy(self):
     """Binding of ADP tp MutS(3thy)
     Reference:  Shikha et al. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops.(2012)
     """
     tmpmol = PDBComplex()
     tmpmol.load_pdb('./pdb/3thy.pdb')
     s = tmpmol.interaction_sets['ADP-A-935']
     # Saltbridge to His295 and Lys675
     saltb = {saltbridge.resnr for saltbridge in s.saltbridge_lneg}
     self.assertTrue({675}.issubset(saltb))
     # pi-stacking interaction with Tyr815
     pistackres = {pistack.resnr for pistack in s.pistacking}
     self.assertTrue({815}.issubset(pistackres))