SMTL ID : 4jnm.1

Discovery of Potent and Efficacious Urea-containing Nicotinamide Phosphoribosyltransferase (NAMPT) Inhibitors with Reduced CYP2C9 Inhibition Properties

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 1LJ: 1-[(6-aminopyridin-3-yl)methyl]-3-[4-(phenylsulfonyl)phenyl]urea(Non-covalent)

1LJ.1: 18 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, 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.8 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.219, A:V.242, A:V.242, A:P.273, A:P.307, A:I.309, A:I.309, A:I.351 Hydrogen bonds: A:R.196, A:S.275, B:D.16 Water bridges: A:Y.195, A:Y.195, A:D.219, A:V.242 pi-Stacking: A:H.191, A:F.193, B:Y.18 1LJ.9: 17 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, V.242, A.244, P.273, S.275, P.307, I.309, R.311, I.351, A.379 Ligands: EDO.16 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.219, B:V.242, B:V.242, B:P.273, B:P.307, B:I.309, B:I.351 Hydrogen bonds: B:R.196, B:S.275, A:D.16 Water bridges: B:Y.195, B:D.219, B:D.219, B:R.311 pi-Stacking: B:H.191, B:F.193, A:Y.18

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

PO4.2: 7 residues within 4Å: Chain A: E.246, H.247, V.277, R.311, D.313 Chain B: Y.18 Ligands: 1LJ.1 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:Y.18, A:H.247 Water bridges: A:R.196, A:R.196, A:R.196, A:E.246, 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.40, R.392, S.398, K.400 Ligands: EDO.14 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.40, A:R.40, A:K.400, A:K.415, B:R.196 Salt bridges: A:R.40, A:R.392, A:K.400 PO4.10: 4 residues within 4Å: Chain B: R.40, R.392, S.398, K.400 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.398, B:S.398 Water bridges: B:F.399, B:K.400, B:K.423, A:R.196, A:D.313, A:D.313, A:D.313, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415 PO4.11: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, A.245, E.246, H.247, R.311, D.313 13 PLIP interactions: 10 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, B:R.311, A:E.149, A:K.400, A:K.400 Salt bridges: B:R.196, B:H.247, B:R.311

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

EDO.4: 4 residues within 4Å: Chain A: F.193, G.383, G.384 Chain B: R.392 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.193, A:G.383, A:G.384, B:R.392 Water bridges: A:G.353, A:V.356, A:G.385 EDO.5: 4 residues within 4Å: Chain A: F.123, V.124, R.434, N.479 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.124, A:R.434 EDO.6: 8 residues within 4Å: Chain A: K.400, C.401, F.414, K.415, S.425 Chain B: H.247, S.248, T.251 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.401, A:S.425, A:S.425, B:T.251 Water bridges: A:N.146, B:E.246, B:S.248 EDO.7: 8 residues within 4Å: Chain A: K.169, E.187, L.212, V.213, N.214, F.215, K.216, R.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.169, A:V.213 EDO.8: 6 residues within 4Å: Chain A: Y.188, H.191, Y.240, S.241, V.242 Ligands: 1LJ.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.191 EDO.12: 4 residues within 4Å: Chain B: G.353, G.383, G.384 Ligands: EDO.14 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.353, B:G.383, B:G.384, A:R.392 Water bridges: B:G.355 EDO.13: 8 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, F.414, K.415, S.425 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.401 Water bridges: B:N.146, B:S.425, B:S.425, A:E.246, A:S.248 EDO.14: 6 residues within 4Å: Chain B: R.311, D.313, G.353, D.354 Ligands: PO4.3, EDO.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.311, B:D.354 Water bridges: B:D.313, A:K.423 EDO.15: 4 residues within 4Å: Chain B: G.315, P.317, D.354, G.355 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.355 Hydrogen bonds: A:K.423 EDO.16: 6 residues within 4Å: Chain B: Y.188, H.191, Y.240, S.241, V.242 Ligands: 1LJ.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.191, B:Y.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gunzner-Toste, J. et al., Discovery of potent and efficacious urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with reduced CYP2C9 inhibition properties. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-05-29

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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