SMTL ID : 4rz8.3 (3 other biounits)

Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.118, T.120, S.158, H.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.118 Water bridges: A:N.118 NAG.2: 4 residues within 4Å: Chain A: D.114, K.115, K.124, N.125 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.124 Hydrogen bonds: A:K.115, A:K.115 NAG.3: 9 residues within 4Å: Chain A: P.96, K.136, L.145, N.146, R.246, C.306, V.307, S.308 Ligands: NAG.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 Water bridges: A:D.95, A:R.246, A:V.307 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.160 Water bridges: A:N.160, A:N.160, A:N.160, A:N.163 NAG.5: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.154 NAG.6: 4 residues within 4Å: Chain A: N.179, Y.198, E.200, V.307 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:Y.198, A:Y.198 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.205 Water bridges: A:N.202, A:N.202 NAG.8: 3 residues within 4Å: Chain A: E.219, N.222, N.223 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253 NAG.10: 5 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261, C.262 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.256 NAG.11: 3 residues within 4Å: Chain A: S.175, N.309 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:S.175, A:S.175

1 x 3ZM: 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide(Non-covalent)

3ZM.12: 18 residues within 4Å: Chain A: V.139, S.140, T.141, D.235, E.237, I.238, S.242, F.243, N.244, F.249, I.285, N.286, M.287, W.288, Q.289, G.290, G.334, I.336 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.139, A:E.237, A:E.237, A:F.249, A:W.288 Hydrogen bonds: A:D.235, A:N.286 Water bridges: A:N.286, A:N.286, A:G.290, A:G.334 pi-Stacking: A:W.288

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

EPE.13: 7 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64, Y.101 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.60 Salt bridges: A:D.64, A:D.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Curreli, F. et al., Structure-Based Design of a Small Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity. J.Med.Chem. (2015)

Release Date

2015-09-09

Peptides

Envelope glycoprotein gp120: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Envelope glycoprotein gp120

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