SMTL ID : 4wq6.1

The crystal structure of human Nicotinamide phosphoribosyltransferase (NAMPT) in complex with N-(4-{(S)-[1-(2-methylpropyl)piperidin-4-yl]sulfinyl}benzyl)furo[2,3-c]pyridine-2-carboxamide inhibitor (compound 21)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x 3TQ: N-(4-{(S)-[1-(2-methylpropyl)piperidin-4-yl]sulfinyl}benzyl)furo[2,3-c]pyridine-2-carboxamide(Non-covalent)

3TQ.1: 19 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, P.273, S.275, P.307, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 Ligands: PO4.2, EDO.7 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.193, A:V.242, A:P.273, A:P.307, A:I.309, A:I.351, B:Y.18 Hydrogen bonds: A:D.219 Water bridges: A:S.275, A:R.311, A:A.379 pi-Stacking: A:H.191, A:F.193, B:Y.18 3TQ.13: 17 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, P.307, I.309, R.311, I.351, A.379 Ligands: PO4.15 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:V.242, B:P.307, B:I.309, B:I.351, A:Y.18 Hydrogen bonds: B:D.219 Water bridges: B:R.311, B:A.379 pi-Stacking: B:H.191, B:F.193, B:F.193, A:Y.18

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: 3TQ.1, PO4.14 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:Y.18, A:H.247, A:D.313 Water bridges: B:E.149, B:K.400, A:R.196, A:R.196, A:H.247, A:H.247, A:S.248, A:R.311 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 5 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: EDO.6 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, B:R.196 Water bridges: A:R.392, A:R.392, A:K.400, A:K.415, A:K.423 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.17 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Water bridges: B:E.149, B:F.399, B:K.400, B:K.415, B:K.423, A:D.313, A:D.313, A:D.354, A:D.354 Salt bridges: B:R.392, B:K.400 Hydrogen bonds: A:R.196 PO4.15: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: 3TQ.13 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.247, A:Y.18 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

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

EDO.4: 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.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 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.6: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:D.393, A:D.393, A:N.396, A:S.398 EDO.7: 5 residues within 4Å: Chain A: Y.188, Y.240, S.241, V.242 Ligands: 3TQ.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.191, A:S.241 EDO.8: 1 residues within 4Å: Chain A: K.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.99 Water bridges: A:K.99 EDO.9: 4 residues within 4Å: Chain A: N.67, K.71, K.229, Y.230 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.71 Water bridges: A:N.67, A:N.67, A:N.67, A:Y.230 EDO.10: 7 residues within 4Å: Chain A: Y.23, K.24, Y.26, P.27, P.28, Y.142 Chain B: H.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.24 EDO.11: 7 residues within 4Å: Chain A: L.62, Q.63, E.121, V.461, K.469, S.470, Y.471 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.121, A:E.121, A:K.469 EDO.12: 6 residues within 4Å: Chain A: F.9, N.10, L.13, A.14 Chain B: Y.195, A.222 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.10, A:L.13 Water bridges: A:E.8, B:Y.195 EDO.16: 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: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:C.401 Water bridges: B:K.400, B:C.401, B:V.413, A:E.246, A:H.247, A:S.248 EDO.17: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.14 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.18: 6 residues within 4Å: Chain B: G.122, F.123, V.124, R.434, F.440, N.479 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.124, B:N.479 EDO.19: 5 residues within 4Å: Chain B: Q.63, N.67, K.71, V.467, S.470 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.67, B:K.71, B:S.470

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zak, M. et al., Identification of nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with no evidence of CYP3A4 time-dependent inhibition and improved aqueous solubility. Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-02-11

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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