SMTL ID : 4kfb.1

HIV-1 reverse transcriptase with bound fragment at NNRTI adjacent site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 1QP: ethyl pyrazolo[1,5-a]pyridine-3-carboxylate(Non-covalent)

1QP.1: 14 residues within 4Å: Chain A: Q.93, Q.163, M.166, T.167, L.170, E.171, A.174, I.182, Y.183, Q.184 Chain B: E.139, T.140, P.141 Ligands: DMS.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.166, A:T.167, A:L.170, A:A.174, B:P.141 Hydrogen bonds: A:Q.93, A:Q.184 Water bridges: A:I.182

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

DMS.2: 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.3: 6 residues within 4Å: Chain A: R.279, Q.280, K.283, Q.336, R.358, K.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.279, A:Q.280 DMS.4: 8 residues within 4Å: Chain A: V.92, Q.93, Y.183 Chain B: N.138, E.139, T.140, P.141 Ligands: 1QP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.93 DMS.5: 8 residues within 4Å: Chain A: N.365, W.403, K.426, L.427, W.428, Y.429, Q.511, D.513 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.428 Salt bridges: A:D.513 DMS.6: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.333, A:Q.336 DMS.8: 4 residues within 4Å: Chain A: Q.87 Chain B: P.56, Y.57, K.127 No protein-ligand interaction detected (PLIP) DMS.9: 6 residues within 4Å: Chain A: T.378, I.382 Chain B: T.28, T.401, W.402, E.405 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.405 DMS.10: 5 residues within 4Å: Chain B: I.245, I.271, Y.272, V.315, N.349 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.349 DMS.11: 9 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 No protein-ligand interaction detected (PLIP) DMS.12: 4 residues within 4Å: Chain B: W.25, E.400, W.403, T.404 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.400

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

T27.7: 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:K.105, A:V.108, A:V.181, 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:L.230

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

2013-05-15

Peptides

REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEA P66 RT: A
P51 RT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEA P66 RT

P51 RT

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