SMTL ID : 4o16.1

Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x 1XC: 6-({4-[(3,5-difluorophenyl)sulfonyl]benzyl}carbamoyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)imidazo[1,2-a]pyridin-1-ium(Non-covalent)

1XC.1: 28 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, G.197, D.219, Y.240, S.241, V.242, A.244, P.273, S.275, I.309, R.311, D.313, I.351, G.353, A.379, G.383, G.384, G.385 Chain B: D.16, Y.18, R.392 Ligands: PO4.2, PO4.9, EDO.10, EDO.12 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.191, A:V.242, A:V.242, A:I.351 Hydrogen bonds: A:D.219, A:D.313, A:G.384, A:G.385 Water bridges: A:R.311, A:R.311, A:G.383 pi-Stacking: A:H.191, A:F.193, A:F.193, B:Y.18 Halogen bonds: A:Y.240 Salt bridges: B:R.392 1XC.17: 28 residues within 4Å: Chain A: D.16, Y.18, R.392 Chain B: Y.188, H.191, F.193, R.196, G.197, D.219, Y.240, S.241, V.242, A.244, P.273, S.275, I.309, R.311, D.313, I.351, G.353, A.379, G.383, G.384, G.385 Ligands: PO4.18, PO4.25, EDO.26, EDO.28 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.191, B:V.242, B:V.242, B:I.351 Hydrogen bonds: B:D.219, B:D.313, B:G.384, B:G.385 Water bridges: B:R.311, B:R.311, B:G.383 pi-Stacking: B:H.191, B:F.193, B:F.193, A:Y.18 Halogen bonds: B:Y.240 Salt bridges: A:R.392

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: 1XC.1, PO4.9 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.247, B:Y.18 Water bridges: A:R.196, A:R.196, A:R.196, A:E.246, A:E.246, A:S.248 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.9: 8 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, F.399, K.400 Ligands: 1XC.1, PO4.2, EDO.10 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.399, A:R.196 Water bridges: B:R.392, B:F.399, B:K.400, B:K.415, B:K.415 Salt bridges: B:R.392, B:K.400 PO4.18: 8 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: 1XC.17, PO4.25 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.247, A:Y.18 Water bridges: B:R.196, B:R.196, B:R.196, B:E.246, B:E.246, B:S.248 Salt bridges: B:R.196, B:H.247, B:R.311 PO4.25: 8 residues within 4Å: Chain A: R.392, S.398, F.399, K.400 Chain B: R.196 Ligands: 1XC.17, PO4.18, EDO.26 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.399, 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

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

EDO.3: 8 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, F.414, K.415, S.425 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Y.23, K.24, Y.26, P.27, P.28, Y.142 Chain B: H.264 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: G.122, F.123, V.124, R.434, F.440, N.479 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: D.192, G.194, Y.195, V.198, A.204, G.207, A.208, T.220, L.387 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: S.180, N.182, N.337, S.338, L.343, E.376 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: E.8, F.9, N.10, L.13, A.14 Chain B: A.222 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: D.313, D.354 Chain B: K.423 Ligands: 1XC.1, PO4.9 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: Y.54, N.164, Q.168, D.357, I.358, L.386 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: Y.188 Ligands: 1XC.1 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: K.53, Y.54, E.55, E.56, E.167, K.170 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: N.67, K.71, K.229, Y.230 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: P.120, F.123, Y.471, E.475, N.479 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: P.120, L.457, H.459 Ligands: EDO.15 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: K.400, C.401, F.414, K.415, S.425 Chain B: H.247, S.248, T.251 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: H.264 Chain B: Y.23, K.24, Y.26, P.27, P.28, Y.142 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: G.122, F.123, V.124, R.434, F.440, N.479 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain B: D.192, G.194, Y.195, V.198, A.204, G.207, A.208, T.220, L.387 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: S.180, N.182, N.337, S.338, L.343, E.376 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: A.222 Chain B: E.8, F.9, N.10, L.13, A.14 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: K.423 Chain B: D.313, D.354 Ligands: 1XC.17, PO4.25 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: Y.54, N.164, Q.168, D.357, I.358, L.386 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain B: Y.188 Ligands: 1XC.17 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: K.53, Y.54, E.55, E.56, E.167, K.170 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: N.67, K.71, K.229, Y.230 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: P.120, F.123, Y.471, E.475, N.479 Ligands: EDO.32 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: P.120, L.457, H.459 Ligands: EDO.31 Ligand excluded by PLIP

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
A

Nicotinamide phosphoribosyltransferase

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