SMTL ID : 4o1d.1

Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x DGB: (2E)-N-{4-[1-(benzenecarbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide(Non-covalent)

DGB.1: 18 residues within 4Å: Chain A: Y.188, R.191, F.193, R.196, D.219, V.242, A.244, P.273, S.275, T.304, Q.305, P.307, I.309, R.311, I.351 Chain B: D.16, Y.18 Ligands: EDO.8 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.193, A:D.219, A:A.244, A:P.273, A:I.351, B:D.16, B:Y.18 Hydrogen bonds: A:S.275 Water bridges: A:A.245 pi-Stacking: A:F.193, B:Y.18 DGB.11: 18 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, R.191, F.193, R.196, D.219, V.242, A.244, P.273, S.275, T.304, Q.305, P.307, I.309, R.311, I.351 Ligands: EDO.15 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.193, B:D.219, B:V.242, B:A.244, B:P.273, B:P.307, B:I.309, B:I.351, A:D.16, A:Y.18 Hydrogen bonds: B:S.275 Water bridges: B:D.219, B:A.245 pi-Stacking: B:F.193, A:Y.18

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

PO4.2: 6 residues within 4Å: Chain A: R.40, R.392, S.398, K.400, K.415 Ligands: EDO.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.398, A:S.398, A:S.398 Water bridges: A:R.392, A:R.392, A:F.399, A:K.400, A:K.400, A:K.415 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.10: 7 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: EDO.4 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.247, A:D.313, B:Y.18 Water bridges: A:R.196, A:R.196, A:R.196, A:H.247, A:S.248, B:E.149, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.12: 6 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: EDO.4, EDO.17 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:R.392, B:F.399, B:K.400, B:K.415, A:D.313, A:D.354 Salt bridges: B:R.392, B:K.400 Hydrogen bonds: A:R.196 PO4.21: 6 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:H.247 Water bridges: B:R.196, B:S.248, B:R.311, B:R.311, A:Y.18, A:Y.18, A:K.400, A:K.400, A:K.400, A:K.400 Salt bridges: B:R.196, B:H.247, B:R.311

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

EDO.3: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.392, A:S.398 EDO.4: 8 residues within 4Å: Chain A: R.311, D.313, G.353, D.354 Chain B: K.423 Ligands: EDO.6, PO4.10, PO4.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.311, A:D.354, B:K.423 Water bridges: A:H.247, A:D.313 EDO.5: 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:N.146, B:C.401, B:V.413 Hydrogen bonds: B:C.401 EDO.6: 5 residues within 4Å: Chain A: D.354, G.355, G.383, G.384 Ligands: EDO.4 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.354, A:D.354, A:G.355, A:G.384 Water bridges: A:F.193, A:V.356, A:V.356, B:R.392, B:R.392 EDO.7: 4 residues within 4Å: Chain A: G.315, P.317, D.354, G.355 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:G.315, A:G.355, B:K.423 EDO.8: 6 residues within 4Å: Chain A: Y.188, R.191, Y.240, S.241, V.242 Ligands: DGB.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.191, A:R.191, A:Y.240 EDO.9: 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:R.434, A:N.479 EDO.13: 3 residues within 4Å: Chain B: G.353, G.383, G.384 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.383, B:G.384 Water bridges: B:G.353, B:V.356, B:V.356, B:G.385, A:R.392 EDO.14: 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.15: 5 residues within 4Å: Chain B: Y.188, R.191, Y.240, S.241 Ligands: DGB.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.191, B:R.191, B:Y.240 Water bridges: B:S.241 EDO.16: 8 residues within 4Å: Chain A: Y.195, Q.201, A.222 Chain B: E.8, F.9, N.10, L.13, A.14 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.8, B:N.10, A:Y.195, A:Y.195 EDO.17: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:N.396, B:S.398 EDO.18: 6 residues within 4Å: Chain B: S.31, K.32, N.136, T.137, D.138, P.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.32, B:N.136 EDO.19: 4 residues within 4Å: Chain B: F.123, V.124, R.434, N.479 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.124, B:R.434, B:N.479 Water bridges: B:R.434 EDO.20: 7 residues within 4Å: Chain B: K.169, E.187, V.213, N.214, F.215, K.216, R.477 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.214 Water bridges: B:K.169

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

Related Entries With Identical Sequence