SMTL ID : 4lv9.1

Fragment-based Identification of Amides Derived From trans-2-(Pyridin-3-yl)cyclopropanecarboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

4 x 20J: 7-chloro-3-methyl-2H-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

20J.1: 10 residues within 4Å: Chain A: F.193, R.196, D.219, S.241, V.242, A.244, A.245, S.275, R.311 Chain B: Y.18 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.219, A:A.244, B:Y.18 Hydrogen bonds: A:S.275, A:S.275, A:R.311 Water bridges: A:A.245 pi-Stacking: A:F.193, B:Y.18 20J.2: 9 residues within 4Å: Chain A: Y.188, H.191, Y.240, S.241, V.242, I.309, R.349, I.351, A.379 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.242, A:I.309, A:R.349 Halogen bonds: A:Y.240 20J.6: 9 residues within 4Å: Chain A: Y.18 Chain B: F.193, D.219, S.241, V.242, A.244, A.245, S.275, R.311 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:D.219, B:A.244, A:Y.18 Hydrogen bonds: B:S.275, B:S.275, B:R.311 pi-Stacking: B:F.193, A:Y.18 20J.7: 9 residues within 4Å: Chain B: Y.188, H.191, Y.240, S.241, V.242, I.309, R.349, I.351, A.379 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.242, B:I.309, B:R.349 Water bridges: B:H.191 Halogen bonds: B:Y.240

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

PO4.3: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.415 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398, A:S.398 Water bridges: A:R.392, A:D.393, A:D.393, A:K.400, A:K.400, A:K.400, A:K.415, A:K.423, B:R.196 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.4: 5 residues within 4Å: Chain A: G.353, G.355, G.383, G.384 Chain B: R.392 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.355, A:G.383, A:G.384, B:R.392 Water bridges: A:D.354, A:V.356, A:V.356, A:V.356, A:G.385, B:D.393 PO4.8: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400, K.423 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.398 Water bridges: B:R.40, B:R.392, B:R.392, B:N.396, B:K.400, B:K.415, B:K.423, A:D.313, A:D.354, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423 PO4.9: 6 residues within 4Å: Chain B: G.353, G.355, V.356, G.383, G.384, G.385 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Water bridges: A:R.392, A:D.393, B:V.356, B:V.356 Hydrogen bonds: B:G.355, B:G.383, B:G.384, B:G.385

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

EDO.5: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.124, A:R.434, A:R.434, A:N.479 EDO.10: 5 residues within 4Å: Chain B: G.128, N.129, K.426, V.441, T.442 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.129, B:K.426, B:T.442 Water bridges: B:E.41, B:G.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Identification of amides derived from 1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-09-25

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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