SMTL ID : 4o1b.1

The crystal structure of a mutant NAMPT (G217R) in complex with an inhibitor APO866

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 19 residues within 4Å: Chain A: G.185, Y.188, K.189, H.191, F.193, R.196, R.217, D.219, V.242, A.244, S.275, I.309, R.311, R.349, I.351, I.378, A.379 Chain B: D.16, Y.18 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.188, A:F.193, A:D.219, A:V.242, A:A.244, A:I.309, A:I.351, A:A.379, B:Y.18 Hydrogen bonds: A:K.189, A:S.275 Water bridges: A:H.191, A:A.245 pi-Stacking: A:F.193, B:Y.18 DGB.9: 18 residues within 4Å: Chain A: D.16, Y.18 Chain B: G.185, Y.188, K.189, H.191, F.193, R.196, R.217, D.219, A.244, S.275, I.309, R.311, R.349, I.351, I.378, A.379 16 PLIP interactions: 3 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:D.16, A:Y.18, B:Y.188, B:F.193, B:D.219, B:A.244, B:I.309, B:I.351, B:A.379 pi-Stacking: A:Y.18, B:F.193 Hydrogen bonds: B:K.189, B:S.275 Water bridges: B:H.191, B:A.245 pi-Cation interactions: B:K.189

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

PO4.2: 6 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: EDO.6, PO4.11 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.398, B:R.196 Water bridges: A:R.392, A:F.399, A:K.400, A:K.415, B:D.313 Salt bridges: A:R.392, A:K.400 PO4.3: 7 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: PO4.10 16 PLIP interactions: 13 interactions with chain A, 3 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, A:R.311, A:R.311, A:R.311, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.10: 6 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: PO4.3, EDO.12 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.196, B:S.398 Water bridges: A:D.313, A:D.313, A:D.313, A:D.354, A:D.354, A:D.354, B:E.149, B:F.399, B:K.400, B:K.415, B:K.423 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: PO4.2 13 PLIP interactions: 8 interactions with chain B, 5 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 Salt bridges: B:R.196, B:H.247, B:R.311

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

EDO.4: 5 residues within 4Å: Chain A: G.353, D.354, G.355, G.383, G.384 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:G.385, B:R.392, B:R.392 EDO.5: 4 residues within 4Å: Chain A: G.315, P.317, D.354, G.355 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.315, A:D.354, A:G.355 EDO.6: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.392, A:N.396, A:S.398 Water bridges: A:R.392, A:R.392 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:G.122, A:V.124, A:R.434 Water bridges: A:R.434 EDO.8: 4 residues within 4Å: Chain A: S.180, G.181, N.182, S.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.182, A:S.338, A:S.338 Water bridges: A:K.339 EDO.12: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:R.392, B:D.393, B:N.396, B:S.398 EDO.13: 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: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.251, A:C.401 Water bridges: B:E.246, B:S.248, A:N.146, A:F.399, A:C.401, A:V.413 EDO.14: 4 residues within 4Å: Chain A: K.423 Chain B: G.315, D.354, G.355 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:G.355 Hydrogen bonds: A:K.423, A:K.423 EDO.15: 6 residues within 4Å: Chain A: H.90, F.91 Chain B: R.217, Y.240, S.241, V.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.217, B:S.241 EDO.16: 4 residues within 4Å: Chain B: G.353, S.382, G.383, G.384 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.353, B:G.383, B:G.384 Water bridges: B:G.355, B:G.355, B:G.355, B:V.356, B:G.385, A:R.392, A:R.392 EDO.17: 3 residues within 4Å: Chain B: K.117, D.456, L.458 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.117, B:D.456 Water bridges: B:L.458, B:T.460

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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