SMTL ID : 9bxy.1

CRYSTAL STRUCTURE OF HIV-1 LM/HS CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH DL-III-117

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 8 residues within 4Å: Chain A: N.120, T.122, G.123, P.124, I.158, S.160, L.163, H.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 NAG.2: 4 residues within 4Å: Chain A: E.42, N.115, K.117, N.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.42, A:E.42, A:K.117 NAG.3: 11 residues within 4Å: Chain A: D.97, P.98, K.138, L.147, N.148, N.246, R.248, C.308, V.309, S.310 Ligands: NAG.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:K.138, A:N.148, A:R.248, A:R.248, A:S.310 NAG.4: 3 residues within 4Å: Chain A: N.162, T.164, N.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.162 Water bridges: A:N.165 NAG.5: 7 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, Q.214, E.217, K.218 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.155, A:I.156, A:K.218, A:K.218 Water bridges: A:N.175, A:Q.214 NAG.6: 6 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, K.305, N.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.181, A:T.183, A:Y.200 Water bridges: A:N.307 NAG.7: 2 residues within 4Å: Chain A: N.204, K.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204 NAG.8: 4 residues within 4Å: Chain A: T.241, M.242, N.255, T.257 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: N.148, S.177, N.311 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.177, A:N.311 Water bridges: A:S.177, A:S.177

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 6 residues within 4Å: Chain A: L.11, C.13, A.32, Q.62, D.66, Y.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.62 Salt bridges: A:D.66, A:D.66

1 x 01: (3S,5R)-1-[4-(1-carbamimidoyl-L-prolyl)piperazine-1-carbonyl]-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)piperidine-3-carboxamide

01.11: 21 residues within 4Å: Chain A: H.64, V.141, S.142, T.143, D.237, E.239, I.240, S.244, F.245, N.246, F.251, I.287, N.288, M.289, W.290, Q.291, G.292, T.293, G.336, M.338, R.339 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.143, A:E.239, A:E.239, A:I.287, A:N.288, A:W.290 Hydrogen bonds: A:D.237, A:D.237, A:N.288, A:Q.291, A:T.293, A:R.339, A:R.339 pi-Stacking: A:W.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, D. et al., Optimization of a Piperidine CD4-Mimetic Scaffold Sensitizing HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity. Acs Med.Chem.Lett. (2024)

Release Date

2025-04-02

Peptides

HIV-1 LM/HS clade A/E CRF01 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 LM/HS clade A/E CRF01 gp120 core

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