SMTL ID : 4o13.1

The crystal structure of NAMPT in complex with GNE-618

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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 13 PLIP interactions: 12 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 Hydrogen bonds: A:R.196, A:D.219 Water bridges: A:R.196, A:R.311, A:R.311 pi-Stacking: A:H.191, A:F.193, B:Y.18 2P1.8: 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: PO4.10 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A 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, B:R.311 pi-Stacking: B:H.191, B:F.193, A:Y.18

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

PO4.2: 8 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: 2P1.1, PO4.9 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.247, B:Y.18, B:Y.18 Water bridges: A:R.196, A:R.196, A:R.196, A:R.196, A:E.246, A:S.248, A:R.311, A:R.311, B:K.400, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311, B:K.400 PO4.3: 4 residues within 4Å: Chain A: R.392, S.398, K.400 Ligands: EDO.4 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.40, A:R.40, A:S.398 Water bridges: A:F.399, A:K.415, A:K.415, A:K.423, B:R.196 Salt bridges: A:R.392, A:K.400, A:K.415 PO4.9: 6 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: PO4.2, EDO.12 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.196 Water bridges: A:D.313, A:D.313, B:E.149, B:R.392, B:R.392, B:F.399, B:K.400, B:K.415 Salt bridges: B:R.392, B:K.400 PO4.10: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: 2P1.8 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Water bridges: A:Y.18, A:K.400, A:K.400, B:R.196, B:R.196, B:R.196, B:S.248 Hydrogen bonds: B:H.247, B:D.313 Salt bridges: B:R.196, B:H.247, B:R.311

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

EDO.4: 6 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397 Ligands: PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.393, A:N.396, A:C.397 Water bridges: A:D.393, A:D.393 EDO.5: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.124, A:R.434, A:R.434 EDO.6: 7 residues within 4Å: Chain A: K.169, E.187, V.213, N.214, F.215, K.216, R.477 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.187, A:E.187, A:V.213 Water bridges: A:K.169, A:K.216 EDO.7: 8 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, F.414, K.415, S.425 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:E.246, A:E.246, A:S.248, B:F.399, B:C.401, B:V.413 Hydrogen bonds: B:C.401 EDO.11: 8 residues within 4Å: Chain A: K.400, C.401, F.414, K.415, S.425 Chain B: H.247, S.248, T.251 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.401, A:F.414, B:T.251 Water bridges: A:N.146, A:F.399, B:E.246, B:S.248 EDO.12: 6 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397 Ligands: PO4.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.40, B:R.392, B:D.393, B:N.396 EDO.13: 5 residues within 4Å: Chain A: D.420, K.423 Chain B: S.314, G.315, D.354 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.420, A:D.420, B:G.315 Water bridges: B:G.315, B:D.354 EDO.14: 6 residues within 4Å: Chain A: Y.195, A.222 Chain B: F.9, N.10, L.13, A.14 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.195, B:N.10, B:N.10 Water bridges: A:V.221

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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