SMTL ID : 2be2.1

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with R221239

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 8 residues within 4Å: Chain A: E.328, Q.340, Y.342, E.344, P.345, F.346, K.347, N.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.328, A:F.346, A:K.347, A:N.348 GLC-FRU.2: 9 residues within 4Å: Chain B: V.21, W.24, R.78, E.79, K.82, K.395, E.399, E.413, W.414 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.395, B:E.399, B:W.414, B:E.79, B:E.79, B:K.82, B:K.82, B:W.414, B:W.414 Water bridges: B:R.78, B:D.76, B:E.79

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: M.230, G.231, W.266 No protein-ligand interaction detected (PLIP) GOL.4: 4 residues within 4Å: Chain A: D.498, S.499, Q.500, Y.501 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.498, A:Q.500, A:Y.501 Water bridges: A:E.478

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

MN.5: 4 residues within 4Å: Chain A: D.443, G.444, E.478, D.498 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.443, A:E.478, A:D.498, H2O.1, H2O.1

1 x R22: 4-(3,5-DIMETHYLPHENOXY)-5-(FURAN-2-YLMETHYLSULFANYLMETHYL)-3-IODO-6-METHYLPYRIDIN-2(1H)-ONE(Non-covalent)

R22.6: 15 residues within 4Å: Chain A: P.95, L.100, K.101, K.103, V.106, V.179, Y.181, Y.188, G.190, F.227, W.229, L.234, H.235, P.236, Y.318 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.95, A:L.100, A:L.100, A:L.100, A:V.106, A:Y.188, A:Y.188, A:Y.188, A:W.229, A:L.234, A:P.236, A:Y.318 Hydrogen bonds: A:K.101, A:K.101, A:K.103 pi-Stacking: A:W.229 Halogen bonds: A:Y.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Himmel, D.M. et al., Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-Nucleoside Inhibitors Effective against a Broad Range of Drug-Resistant Strains. J.Med.Chem. (2005)

Release Date

2005-12-06

Peptides

REVERSE TRANSCRIPTASE P66 SUBUNIT: A
REVERSE TRANSCRIPTASE P51 SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

REVERSE TRANSCRIPTASE P66 SUBUNIT

REVERSE TRANSCRIPTASE P51 SUBUNIT

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