SMTL ID : 4icl.1

HIV-1 reverse transcriptase with bound fragment at the incoming dNTP binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: 18 residues within 4Å: Chain A: P.97, L.102, K.103, K.104, K.105, V.108, V.181, Y.183, Y.190, G.192, P.227, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.139 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.97, A:K.105, A:V.108, A:Y.183, A:Y.183, A:Y.183, A:Y.183, A:Y.190, A:W.231, A:L.236, A:Y.320 Hydrogen bonds: A:K.103, A:K.103, A:Y.190 Water bridges: A:I.182

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.445, D.500, A.540, D.551 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.445, A:D.500, A:D.551

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: 9 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.527, I.528, K.530, E.531, K.532, V.533 No protein-ligand interaction detected (PLIP) DMS.5: 4 residues within 4Å: Chain A: K.333, G.335, Q.336, K.514 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.336, A:Q.336, A:K.514 Water bridges: A:G.337 DMS.6: 4 residues within 4Å: Chain A: R.450, T.475, N.476, Q.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.476, A:Q.477 DMS.8: 8 residues within 4Å: Chain A: T.378, I.382, T.388 Chain B: T.28, K.31, T.401, W.402, E.405 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.405 DMS.9: 5 residues within 4Å: Chain A: K.13, Q.87 Chain B: P.56, Y.57, K.127 No protein-ligand interaction detected (PLIP) DMS.10: 11 residues within 4Å: Chain A: I.382, V.383, G.386 Chain B: P.26, L.27, I.32, P.134, S.135, I.136, N.137, N.138 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.137, B:N.138, B:N.138 DMS.11: 3 residues within 4Å: Chain B: L.235, H.236, W.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.236, B:W.240 DMS.12: 5 residues within 4Å: Chain B: W.25, E.400, W.403, T.404, W.415 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.403 Water bridges: B:W.415 Salt bridges: B:E.400 pi-Cation interactions: B:W.25 DMS.13: 8 residues within 4Å: Chain A: Q.502, W.537 Chain B: N.266, W.267, Q.270, L.423, V.424, W.427 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.427 DMS.14: 8 residues within 4Å: Chain B: P.244, I.245, V.246, K.264, W.267, W.427, Y.428, Q.429 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.246, B:K.264

1 x 14N: 4-(4-methylpiperazin-1-yl)benzoic acid(Non-covalent)

14N.7: 11 residues within 4Å: Chain A: M.43, R.74, K.75, G.114, Y.117, F.118, Y.148, L.151, P.152, Q.153, D.187 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.117, A:Q.153 Hydrogen bonds: A:Q.153 Water bridges: A:Y.148 Salt bridges: A:K.75, A:D.187 pi-Stacking: A:F.118

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

Reverse transcriptase/ribonuclease H: A
p51 RT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase/ribonuclease H

p51 RT

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