SMTL ID : 4lww.1

Discovery of Potent and Efficacious Cyanoguanidine-containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x LWW: N-(4-(phenylsulfonyl)benzyl)-1H-pyrrolo[3,2-c]pyridine-2-carboxamide(Non-covalent)

LWW.1: 15 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.188, A:F.193, A:V.242, A:V.242, A:I.309, B:Y.18 Hydrogen bonds: A:D.219, A:D.219, A:S.241 Water bridges: A:R.311 pi-Stacking: A:H.191, A:F.193, A:F.193, B:Y.18 LWW.13: 15 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, S.275, I.309, R.311, I.351, A.379 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.188, B:F.193, B:V.242, B:V.242, B:I.309, A:Y.18 Hydrogen bonds: B:D.219, B:D.219, B:S.241, B:S.275 Water bridges: B:R.311 pi-Stacking: B:H.191, B:F.193, B:F.193, A:Y.18

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: PO4.14 14 PLIP interactions: 11 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, 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.4, EDO.16 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.398, A:S.398, B:R.196 Water bridges: A:R.392, A:R.392, A:F.399, A:K.400, A:K.415, A:K.415, B:R.196 Salt bridges: A:R.392, A:K.400 PO4.14: 6 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: PO4.2, EDO.20 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:R.196, B:K.415 Water bridges: A:R.196, A:D.313, A:D.313, B:E.149, B:R.392, B:R.392, B:R.392, B:F.399, B:K.400, B:K.423 Salt bridges: B:R.392, B:K.400 PO4.15: 6 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.247 Water bridges: B:R.196, B:R.196, B:R.196, B:S.248, B:R.311, A:K.400, A:K.400, A:K.400 Salt bridges: B:R.196, B:H.247, B:R.311

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

EDO.4: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.3 Ligand excluded by PLIP EDO.5: 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.6: 7 residues within 4Å: Chain A: E.8, F.9, N.10, L.13, A.14 Chain B: Y.195, A.222 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: G.383, G.384 Chain B: R.392 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: G.315, P.317, D.354, G.355 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: S.31, K.32, N.136, T.137, D.138, P.139 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: F.123, V.124, R.434, N.479 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: Y.103, K.107, E.140 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: I.171, I.358, N.359, Q.362 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: R.392 Chain B: R.311, D.313, G.353, D.354 Ligands: PO4.3, EDO.17 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: R.392 Chain B: G.383, G.384 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: K.423 Chain B: G.315, P.317, D.354, G.355 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: K.228, K.229, Y.231 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.14 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: K.169, E.187, V.213, N.214, F.215, K.216, R.477 Ligand excluded by PLIP EDO.22: 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.23: 6 residues within 4Å: Chain B: S.31, K.32, N.136, T.137, D.138, P.139 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: Y.195, A.222 Chain B: E.8, F.9, N.10, L.13, A.14 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: S.180, G.181, N.182, S.338, K.339 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Discovery of potent and efficacious cyanoguanidine-containing nicotinamide phosphoribosyltransferase (Nampt) inhibitors. Bioorg.Med.Chem.Lett. (2014)

Release Date

2013-12-25

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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