SMTL ID : 4o15.1

The crystal structure of a mutant NAMPT (S165F) in complex with GNE-618

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 2P1: N-(4-{[3-(trifluoromethyl)phenyl]sulfonyl}benzyl)-2H-pyrazolo[3,4-b]pyridine-5-carboxamide(Non-covalent)

2P1.1: 17 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, G.217, D.219, Y.240, S.241, V.242, A.244, S.275, I.309, R.311, I.351 Chain B: D.16, Y.18 Ligands: PO4.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.191, A:F.193, A:V.242, A:V.242, A:I.309, A:I.351 Hydrogen bonds: A:R.196, A:D.219 Water bridges: A:R.196, A:R.311 pi-Stacking: A:F.193, B:Y.18 2P1.5: 18 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, G.217, D.219, Y.240, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 Ligands: PO4.7 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B pi-Stacking: A:Y.18, B:F.193 Hydrophobic interactions: B:H.191, B:F.193, B:V.242, B:V.242, B:I.309, B:I.351 Hydrogen bonds: B:R.196, B:D.219 Water bridges: B:R.196, B:R.311

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: 2P1.1 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.247, A:D.313, B:Y.18, B:Y.18 Water bridges: A:R.196, A:R.196, A:R.196, A:H.247, A:S.248, B:K.400, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 4 residues within 4Å: Chain A: R.40, R.392, S.398, K.400 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.398, A:S.398, A:S.398, A:K.415 Water bridges: A:R.40, A:R.392, A:R.392, A:N.396, A:C.397, A:F.399, A:K.400 Salt bridges: A:R.40, A:R.392, A:K.400 PO4.6: 5 residues within 4Å: Chain B: R.40, R.392, S.398, K.400, K.415 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.398, B:S.398 Water bridges: B:R.392, B:R.392, B:K.400, B:K.400, B:K.415, B:K.415, A:R.196 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415 PO4.7: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: 2P1.5 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Water bridges: A:Y.18, A:K.400, A:K.400, A:K.400, A:K.400, B:R.196, B:R.196, B:S.248 Hydrogen bonds: B:H.247 Salt bridges: B:R.196, B:H.247, B:R.311

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

EDO.4: 8 residues within 4Å: Chain A: D.192, G.194, Y.195, V.198, A.204, G.207, A.208, T.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.194, A:G.194, A:G.207 EDO.8: 8 residues within 4Å: Chain A: K.400, C.401, F.414, K.415, S.425 Chain B: H.247, S.248, T.251 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.401, B:T.251 Water bridges: A:N.146, A:F.399, A:C.401, A:V.413, B:E.246, B:S.248 EDO.9: 8 residues within 4Å: Chain B: D.192, G.194, Y.195, V.198, A.204, G.207, A.208, T.220 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.194, B:G.194, B:G.207, B:T.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors. Plos One (2014)

Release Date

2014-10-22

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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