SMTL ID : 8dxk.1

HIV-1 reverse transcriptase/rilpivirine with bound fragment 4-bromopyrazole at multiple sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 15 residues within 4Å: Chain A: P.97, L.102, K.103, K.105, V.108, V.181, Y.183, Y.190, F.229, W.231, L.236, H.237, P.238, Y.320 Chain B: E.138 18 PLIP interactions: 18 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.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

6 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.14: 4 residues within 4Å: Chain B: W.24, E.399, W.402, T.403 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.399 DMS.15: 4 residues within 4Å: Chain A: Q.87 Chain B: P.55, Y.56, K.126 No protein-ligand interaction detected (PLIP) DMS.16: 6 residues within 4Å: Chain A: T.378, T.388 Chain B: T.27, T.400, W.401, E.404 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.404 DMS.17: 4 residues within 4Å: Chain B: N.265, W.266, Q.269, W.426 No protein-ligand interaction detected (PLIP) DMS.18: 7 residues within 4Å: Chain B: P.243, I.244, V.245, K.263, W.426, Y.427, Q.428 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.245, B:K.263

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: I.7, E.8, V.10, S.164, S.165, K.168 Chain B: P.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.164 Water bridges: A:S.165 EDO.4: 6 residues within 4Å: Chain A: K.426, L.427, W.428, Y.429, Q.511, D.513 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.428, A:Y.429, A:Y.429, A:D.513 EDO.19: 6 residues within 4Å: Chain B: I.31, V.35, I.132, P.133, S.134, I.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.132 Water bridges: B:T.139

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.445, D.500, H.541, D.551 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.445, A:D.551, H2O.5, H2O.9, H2O.12

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: R.279, Q.280, K.283, Q.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.280 Water bridges: A:R.279 Salt bridges: A:R.279, A:K.283 SO4.7: 5 residues within 4Å: Chain A: K.478, E.516, S.517, E.518, L.519 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.516, A:E.518, A:L.519 Water bridges: A:S.517 Salt bridges: A:K.478 SO4.8: 3 residues within 4Å: Chain A: K.333, G.335, Q.336 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.336 Water bridges: A:K.333, A:K.333, A:K.333, A:G.337 Salt bridges: A:K.333 SO4.20: 4 residues within 4Å: Chain B: L.234, H.235, W.239 Ligands: BYZ.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.235, B:H.235

8 x BYZ: 4-bromo-1H-pyrazole(Non-covalent)

BYZ.9: 7 residues within 4Å: Chain A: I.7, S.119, V.120, M.166, I.169, W.214, L.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.119 Water bridges: A:I.7, A:I.7, A:I.7, A:I.7 BYZ.10: 4 residues within 4Å: Chain A: T.167, E.171, A.174 Chain B: P.140 No protein-ligand interaction detected (PLIP) BYZ.11: 8 residues within 4Å: Chain A: T.405, E.406, Y.407, W.408 Chain B: K.331, Q.332, G.333, K.424 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.406, A:W.408 BYZ.12: 7 residues within 4Å: Chain A: Q.93, G.95, I.96, P.97, Y.183 Chain B: N.137, P.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.183 BYZ.13: 5 residues within 4Å: Chain A: R.358, G.361, K.514, S.515, E.516 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.514 Water bridges: A:R.358, A:R.358, A:R.358 BYZ.21: 10 residues within 4Å: Chain A: I.382, V.383 Chain B: P.25, L.26, I.31, P.133, S.134, I.135, N.136, N.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.26 Water bridges: B:N.136 Halogen bonds: B:N.137 BYZ.22: 7 residues within 4Å: Chain B: Y.232, L.234, W.239, Y.354, K.374, E.378 Ligands: SO4.20 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.339 pi-Cation interactions: B:K.374 Halogen bonds: B:Y.232 BYZ.23: 9 residues within 4Å: Chain B: L.74, V.75, D.76, F.77, R.78, G.152, T.409, W.410, I.411 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.75, B:F.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chopra, A. et al., Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. J.Med.Chem. (2023)

Release Date

2023-05-31

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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