SMTL ID : 8a1q.1

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor STP0404 (Pirmitegravir)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: P.20, K.22, Q.34, D.35, N.36 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.20, A:K.22, A:Q.34, A:N.36 Water bridges: A:N.36 EDO.2: 3 residues within 4Å: Chain A: K.48 Chain D: Q.189 Ligands: WBV.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.49 EDO.3: 3 residues within 4Å: Chain B: E.113, G.139, S.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.113, B:S.140 EDO.4: 4 residues within 4Å: Chain B: Q.116, E.117 Chain D: K.194 Ligands: WBV.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.194 EDO.5: 5 residues within 4Å: Chain B: E.106, E.108, F.121, K.124 Chain D: R.128 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.106, B:A.107, B:F.121, D:R.128 EDO.6: 6 residues within 4Å: Chain B: G.218, V.222 Chain D: R.128, P.130, I.225 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain B: E.113, T.114, G.115, S.140, N.141 Ligands: WBV.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.113, B:G.115, B:S.140 Water bridges: B:Q.116 EDO.8: 4 residues within 4Å: Chain B: K.194 Chain D: Q.116, E.117 Ligands: WBV.10 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.194, D:Q.116 EDO.9: 9 residues within 4Å: Chain B: N.205, K.206, G.218 Chain D: A.126, G.127, R.128, W.129, P.130 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.206, B:K.206 EDO.12: 6 residues within 4Å: Chain B: Q.189 Chain C: I.49, I.50, R.51 Chain D: W.153 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.51 Water bridges: C:I.49 EDO.13: 7 residues within 4Å: Chain B: D.188, Q.189, A.190, E.191 Chain C: K.48 Ligands: WBV.10, EDO.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.191, C:K.48 EDO.15: 6 residues within 4Å: Chain B: R.128 Chain D: E.106, A.107, E.108, F.121, K.124 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.128, D:E.106, D:F.121 EDO.16: 4 residues within 4Å: Chain B: Y.120 Chain D: V.109, P.111, K.194 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain D: H.88, L.89, E.90, G.91 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.91 EDO.18: 7 residues within 4Å: Chain D: E.113, T.114, G.115, S.140, N.141, S.144 Ligands: WBV.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.113, D:G.115 Water bridges: D:Q.116

2 x WBV: (2S)-tert-butoxy{4-(4-chlorophenyl)-2,3,6-trimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid(Non-covalent)

WBV.10: 20 residues within 4Å: Chain B: A.190, E.191, H.192, T.195, M.199 Chain C: Y.8, W.17, K.48, I.50 Chain D: Q.116, Y.120, L.123, T.145, T.146, A.149, A.150, W.153 Ligands: EDO.8, EDO.13, EDO.18 15 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: B:T.195, D:Q.116, D:Y.120, D:L.123, D:T.146, C:Y.8, C:W.17, C:K.48, C:I.50 Hydrogen bonds: B:E.191, B:H.192, B:T.195 Salt bridges: B:H.192, C:K.48 pi-Cation interactions: C:K.48 WBV.14: 19 residues within 4Å: Chain A: Y.8, W.17, K.48, I.50 Chain B: Q.116, Y.120, T.145, T.146, A.149, A.150, W.153 Chain D: A.190, E.191, H.192, T.195, M.199 Ligands: EDO.2, EDO.4, EDO.7 17 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: D:T.195, A:Y.8, A:W.17, A:K.48, A:I.50, B:Q.116, B:Y.120, B:T.146, B:A.149 Hydrogen bonds: D:E.191, D:H.192, D:T.195, D:T.195, B:Q.116 Salt bridges: D:H.192 pi-Stacking: A:W.17 pi-Cation interactions: A:K.48

2 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 2 residues within 4Å: Chain B: D.85, D.137 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.85, B:D.137, H2O.1, H2O.1, H2O.2 MG.19: 2 residues within 4Å: Chain D: D.85, D.137 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.85, D:D.137, H2O.3, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singer, M.R. et al., The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. Mbio (2023)

Release Date

2023-02-01

Peptides

Integrase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrase

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