SMTL ID : 6aoc.1 (1 other biounit)

Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.445, E.480, D.500 Ligands: MN.2, ZW2.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.445, A:E.480, A:D.500, A:D.500 MN.2: 4 residues within 4Å: Chain A: D.445, D.551 Ligands: MN.1, ZW2.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.445, A:D.551, H2O.3, H2O.4

1 x ZW2: 6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

ZW2.3: 9 residues within 4Å: Chain A: D.445, G.446, E.480, D.500, A.540, H.541, D.551 Ligands: MN.1, MN.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.540 Hydrogen bonds: A:H.541

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 4 residues within 4Å: Chain A: Q.396, K.397, E.398, F.418 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.397, A:E.398 PGE.19: 12 residues within 4Å: Chain B: V.76, D.77, F.78, R.79, N.82, G.153, Y.184, M.185, T.387, W.411, I.412 Ligands: EDO.34 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.76, B:F.78, B:N.82, B:T.387 Water bridges: B:T.387, B:E.414 PGE.20: 12 residues within 4Å: Chain B: K.31, I.64, K.65, K.66, K.67, D.68, S.69, T.404, E.405, W.407, Q.408 Ligands: EDO.38 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.31, B:K.31, B:K.65, B:D.68, B:D.68, B:Q.408 PGE.21: 11 residues within 4Å: Chain B: K.66, K.67, D.187, Y.189, Y.233, T.378, Q.408, A.409, W.411 Ligands: EDO.25, EDO.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.67, B:T.378 PGE.22: 6 residues within 4Å: Chain B: I.95, P.96, P.98, I.181, Y.182, Q.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.183

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

EDO.5: 4 residues within 4Å: Chain A: K.390, F.391, E.415, E.417 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: K.103, K.104, K.105, V.108, Y.190, H.237, P.238, Y.320 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: K.463, R.465 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: R.279, K.283, R.286 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: Q.375, K.376, T.379 Chain B: T.401 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: T.405, E.406, Y.407, W.408 Chain B: K.332, G.334, K.425 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: A.439, E.440, N.462, K.463 Chain B: A.289 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: R.450, T.475, N.476, Q.477 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: K.478, S.517, E.518, L.519 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: G.543, G.545, E.548, K.552 Chain B: R.285 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Q.549, K.552, L.553 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: T.340, Y.341, Q.342, T.353, G.354 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: Q.332, Q.334, T.340, Q.342 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: K.333, G.335, Q.336, G.337, W.339, D.366, Q.369 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: W.25, E.400, W.403, T.404 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: W.25, R.79, E.400, W.415 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain B: K.67, Y.233, E.371, Q.374, K.375, T.378 Ligands: PGE.21, EDO.26 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: W.240, Y.355, K.375, E.379 Ligands: EDO.25 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: K.66, V.109, L.110, D.111, D.187, T.410 Ligands: PGE.21 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: E.329, I.330, Q.331, P.393, P.422 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: T.405 Chain B: G.334, Q.335, G.336, H.362 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain B: I.6, E.7, T.8, V.9, V.119, I.160, S.163 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain B: P.2, I.3, S.4, P.120, R.126, N.148, V.149 Ligands: EDO.32 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: S.4, P.5, F.117, S.118, V.149 Ligands: EDO.31 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: E.171 Chain B: E.43, K.50 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: N.82, K.155, Y.184, M.185 Ligands: PGE.19 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: I.95, P.158, Y.182, Q.183, Y.184, M.185 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: E.54, N.55, P.56, K.127 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain B: F.417, N.419 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain B: R.359, K.367, E.405, Y.406, Q.408 Ligands: PGE.20 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain A: T.378, I.382 Chain B: T.28, T.401, W.402, E.405 Ligands: EDO.41 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain B: T.241, V.242, Q.243, Y.340, G.353, K.354, Y.355 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: W.25, P.26, L.27, T.28, T.404 Ligands: EDO.39 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kankanala, J. et al., Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H. Eur J Med Chem (2017)

Release Date

2018-08-08

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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