SMTL ID : 4ifv.1

Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-Ray Crystallographic Fragment Screening

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

1 x T27: 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile(Non-covalent)

T27.1: 16 residues within 4Å: Chain A: P.97, L.102, K.103, K.105, V.108, V.181, Y.183, Y.190, P.227, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.139 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.97, A:L.102, A:K.105, A:V.108, A:V.181, A:Y.183, A:Y.183, A:Y.183, A:Y.183, A:Y.183, A:Y.190, A:Y.190, A:W.231, A:L.236, A:Y.320 Hydrogen bonds: A:K.103, A:K.103 Water bridges: A:I.182, A:Y.190

2 x FMQ: [1-(4-fluorophenyl)-5-methyl-1H-pyrazol-4-yl]methanol(Non-covalent)

FMQ.2: 7 residues within 4Å: Chain A: V.469, L.471, Q.482, L.486, E.518, L.519, Q.522 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.471, A:Q.482, A:Q.482, A:L.486, A:L.519 Hydrogen bonds: A:Q.482, A:E.518 FMQ.8: 9 residues within 4Å: Chain A: T.379, I.382 Chain B: W.25, P.26, E.400, T.401, W.403, T.404 Ligands: DMS.9 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.379, B:W.25, B:W.25, B:P.26, B:E.400 Hydrogen bonds: B:E.400 Water bridges: B:W.415 pi-Stacking: B:W.25

11 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 8 residues within 4Å: Chain A: N.365, W.403, K.426, L.427, W.428, Y.429, Q.511, D.513 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.367 Salt bridges: A:D.513 pi-Cation interactions: A:Y.429 DMS.4: 7 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.527, I.528, K.530, E.531 No protein-ligand interaction detected (PLIP) DMS.5: 3 residues within 4Å: Chain A: K.333, G.335, Q.336 No protein-ligand interaction detected (PLIP) DMS.6: 3 residues within 4Å: Chain A: T.475, N.476, Q.477 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.475, A:N.476, A:Q.477 DMS.9: 7 residues within 4Å: Chain A: T.378, T.388 Chain B: T.28, T.401, W.402, E.405 Ligands: FMQ.8 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.405 DMS.10: 4 residues within 4Å: Chain A: Q.87 Chain B: P.56, Y.57, K.127 No protein-ligand interaction detected (PLIP) DMS.11: 10 residues within 4Å: Chain A: I.382, V.383 Chain B: P.26, L.27, I.32, P.134, S.135, I.136, N.137, N.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.137, B:N.138 DMS.12: 3 residues within 4Å: Chain B: L.235, H.236, W.240 No protein-ligand interaction detected (PLIP) DMS.13: 4 residues within 4Å: Chain A: Q.502 Chain B: Q.270, L.423, W.427 No protein-ligand interaction detected (PLIP) DMS.14: 8 residues within 4Å: Chain B: Q.243, P.244, I.245, V.246, K.264, W.427, Y.428, Q.429 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.246, B:K.264 DMS.15: 7 residues within 4Å: Chain B: Q.243, I.245, I.271, Y.272, V.315, N.349, T.352 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: D.445, D.500, D.551 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.445, A:D.551, H2O.7, H2O.11, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauman, J.D. et al., Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening. J.Med.Chem. (2013)

Release Date

2013-02-06

Peptides

Exoribonuclease H, p66 RT: A
Gag-Pol polyprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exoribonuclease H, p66 RT

Gag-Pol polyprotein

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