SMTL ID : 4ztj.1

Crystal Structure of the Prototype Foamy Virus Intasome with a 2-Pyridinone Aminal Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 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.13: 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.165, T.166, S.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.165, A:T.166, A:S.167 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.10: 6 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, D.276 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.270, B:D.276, A:Q.299, A:Q.299 GOL.12: 6 residues within 4Å: Chain A: V.263, Y.306 Chain C: C.6, A.7, T.8 Chain D: C.11 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain E: S.165, T.166, S.167 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.165, E:T.166, E:T.166, E:S.167 Water bridges: E:T.166 GOL.15: 4 residues within 4Å: Chain E: P.138, S.139, Q.140, K.244 No protein-ligand interaction detected (PLIP) GOL.22: 6 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, D.276 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.299, E:Q.299, F:Q.270, F:D.276 GOL.24: 6 residues within 4Å: Chain E: V.263, Y.306 Chain G: C.6, A.7, T.8 Chain H: C.11 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.5, 4RT.8 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.2, 4RT.8 MG.5: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.4, 4RT.8 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.7, 4RT.8 MG.11: 2 residues within 4Å: Chain B: D.131, D.188 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.188 MG.16: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.17, 4RT.20 5 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:D.131, E:D.188, H2O.8, H2O.9, 4RT.20 MG.17: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.16, 4RT.20 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.14, 4RT.20 MG.23: 2 residues within 4Å: Chain F: D.131, D.188 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 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain A Water bridges: E:K.231, E:K.231, E:K.231, A:R.339 Salt bridges: E:K.231, A:R.339 Hydrogen bonds: A:S.335, 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 SO4.9: 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 SO4.18: 5 residues within 4Å: Chain A: K.231 Chain D: A.17 Chain E: S.335, L.336, R.339 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:S.335, E:L.336 Water bridges: E:R.339, A:K.231, A:K.231, A:K.231 Salt bridges: E:R.339, A:K.231 SO4.19: 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 SO4.21: 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 4RT: (1R,2S,5R)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-1-(hydroxymethyl)-2'-methyl-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione(Non-covalent)

4RT.8: 12 residues within 4Å: Chain A: D.131, D.188, G.190, Y.215, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.4, MG.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.217, A:P.217 Hydrogen bonds: A:D.131 Water bridges: A:Y.132, A:D.188, A:Y.215, A:N.227 4RT.20: 12 residues within 4Å: Chain E: D.131, D.188, G.190, Y.215, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.16, MG.17 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:P.217, E:P.217 Hydrogen bonds: E:D.131 Water bridges: E:Y.132, E:Y.215, E:N.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raheem, I.T. et al., Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors. J.Med.Chem. (2015)

Release Date

2015-10-07

Peptides

PFV INTEGRASE: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

PFV INTEGRASE

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