SMTL ID : 5uoq.1

CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2- PYRIDINONE AMINAL INHIBITOR (COMPOUND 31)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-tetramer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.65, H.69, C.99, C.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.65, A:H.69, A:C.99, A:C.102 ZN.14: 4 residues within 4Å: Chain E: H.65, H.69, C.99, C.102 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.65, E:H.69, E:C.99, E:C.102

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.165, T.166, S.167 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.165, A:T.166, A:S.167, A:T.197, A:T.197 Water bridges: A:T.166 GOL.3: 4 residues within 4Å: Chain A: P.138, S.139, Q.140, K.244 No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain A: Y.132, G.134, Y.144 Chain D: A.17 Ligands: MG.4, 8G1.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.134 GOL.11: 6 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, D.276 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.299, A:Q.299, B:D.276 GOL.13: 7 residues within 4Å: Chain A: V.263, Y.306 Chain C: C.6, A.7, T.8 Chain D: C.11, A.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.306 GOL.15: 3 residues within 4Å: Chain E: S.165, T.166, S.167 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.165, E:T.166, E:T.166, E:S.167, E:T.197 Water bridges: E:T.166 GOL.16: 4 residues within 4Å: Chain E: P.138, S.139, Q.140, K.244 No protein-ligand interaction detected (PLIP) GOL.21: 6 residues within 4Å: Chain E: Y.132, G.134, Y.144 Chain H: A.17 Ligands: MG.17, 8G1.22 1 PLIP interactions: 1 interactions with chain E Water bridges: E:G.134 GOL.24: 6 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, D.276 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Q.299, E:Q.299, F:D.276 GOL.26: 7 residues within 4Å: Chain E: V.263, Y.306 Chain G: C.6, A.7, T.8 Chain H: C.11, A.12 2 PLIP interactions: 2 interactions with chain E Water bridges: E:Y.306, E:Y.306

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.5, GOL.8, 8G1.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.2 MG.5: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.4, 8G1.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.7 MG.12: 3 residues within 4Å: Chain B: D.131, D.188, P.217 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.188 MG.17: 5 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.18, GOL.21, 8G1.22 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.8, H2O.9 MG.18: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.17, 8G1.22 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.14 MG.25: 3 residues within 4Å: Chain F: D.131, D.188, P.217 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.188

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: S.335, L.336, R.339 Chain E: K.231 Chain H: A.17 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Water bridges: E:P.135, E:K.231, A:R.339 Salt bridges: E:K.231, A:R.339 Hydrogen bonds: A:L.336 SO4.7: 3 residues within 4Å: Chain A: H.341, K.342, H.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.342 Salt bridges: A:H.341, A:K.342, A:H.360 SO4.10: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.263 Salt bridges: B:K.222, B:R.225 SO4.19: 5 residues within 4Å: Chain A: K.231 Chain D: A.17 Chain E: S.335, L.336, R.339 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:L.336 Water bridges: E:R.339, A:P.135, A:K.231 Salt bridges: E:R.339, A:K.231 SO4.20: 3 residues within 4Å: Chain E: H.341, K.342, H.360 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.342 Water bridges: E:H.360 Salt bridges: E:H.341, E:K.342, E:H.360 SO4.23: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.263 Salt bridges: F:K.222, F:R.225

2 x 8G1: (3R)-8-[(3-chloro-4-fluorophenyl)methyl]-6-hydroxy-1,5,7-trioxo-1,2',3',5,7,8,9,10-octahydro-2H-spiro[imidazo[5,1-a][2,6]naphthyridine-3,1'-indene]-7'-carbonitrile(Non-covalent)

8G1.9: 12 residues within 4Å: Chain A: D.131, D.188, G.190, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.4, MG.5, GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.217, A:P.217 Water bridges: A:Y.132, A:N.227 8G1.22: 12 residues within 4Å: Chain E: D.131, D.188, G.190, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.17, MG.18, GOL.21 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:P.217, E:P.217 Water bridges: E:Y.132, E:N.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schreier, J.D. et al., Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV. Bioorg. Med. Chem. Lett. (2017)

Release Date

2017-03-29

Peptides

INTEGRASE: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

INTEGRASE

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