SMTL ID : 4o28.1

Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 1QS: N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-6-carboxamide(Non-covalent)

1QS.1: 18 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, P.273, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 Ligands: PO4.2 11 PLIP interactions: 10 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.351 Hydrogen bonds: A:D.219 Water bridges: A:R.311 pi-Stacking: A:H.191, A:F.193, B:Y.18 Halogen bonds: A:Y.240 1QS.9: 17 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, P.273, S.275, I.309, R.311, I.351, A.379 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.191, B:V.242, B:V.242, B:I.351 Hydrogen bonds: B:D.219 Water bridges: B:R.311 pi-Stacking: B:H.191, B:F.193, A:Y.18 Halogen bonds: B:Y.240

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: 1QS.1 15 PLIP interactions: 11 interactions with chain A, 4 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, B:K.400, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 6 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: EDO.5, PO4.11 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398, B:R.196 Water bridges: A:R.392, A:F.399, A:K.400, A:K.415, A:K.415 Salt bridges: A:R.392, A:K.400 PO4.10: 5 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: EDO.15 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.398, A:R.196 Water bridges: B:E.149, B:F.399, B:K.400, B:K.415, B:K.415, B:K.415, A:D.313, A:D.313 Salt bridges: B:R.392, B:K.400 PO4.11: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: PO4.3 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:Y.18, B:H.247 Water bridges: A:K.400, A:K.400, A:K.400, B:R.196, B:R.196, B:R.196, B:S.248 Salt bridges: B:R.196, B:H.247, B:R.311

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

EDO.4: 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: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.251, A:C.401 Water bridges: B:E.246, B:E.246, B:S.248, A:N.146, A:C.401, A:V.413 EDO.5: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.392, A:D.393, A:D.393, A:N.396, A:S.398 EDO.6: 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.7: 4 residues within 4Å: Chain A: F.123, V.124, R.434, N.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.124, A:R.434, A:N.479 Water bridges: A:R.434 EDO.8: 7 residues within 4Å: Chain A: K.169, E.187, V.213, N.214, F.215, K.216, R.477 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.213 EDO.12: 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 EDO.13: 6 residues within 4Å: Chain A: V.198, S.199, K.389 Chain B: V.198, S.199, T.203 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.199, A:S.199, A:K.389, B:S.199, B:S.199 EDO.14: 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.15: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:R.392, B:R.392, B:D.393, B:N.396, B:S.398, B:S.398 Water bridges: B:K.400 EDO.16: 4 residues within 4Å: Chain B: G.315, P.317, D.354, G.355 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.315 EDO.17: 4 residues within 4Å: Chain A: P.27, T.406 Chain B: W.253, H.257 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.253 Water bridges: A:P.28 EDO.18: 6 residues within 4Å: Chain A: S.241, V.242, P.243, V.272 Chain B: F.91, D.93 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:S.241, A:S.241, B:F.91 Hydrogen bonds: B:D.93 EDO.19: 5 residues within 4Å: Chain A: A.222 Chain B: F.9, N.10, L.13, A.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.10, B:N.10

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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