SMTL ID : 5u2m.1

Crystal structure of human NAMPT with A-1293201

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x 7T7: N-[4-({[(3S)-oxolan-3-yl]methyl}carbamoyl)phenyl]-1,3-dihydro-2H-isoindole-2-carboxamide(Non-covalent)

7T7.1: 16 residues within 4Å: Chain A: Y.180, H.183, F.185, R.188, D.211, V.234, A.236, P.265, S.267, I.301, R.303, I.343, A.371 Chain B: D.8, Y.10 Ligands: SO4.2 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A pi-Stacking: B:Y.10, A:F.185 Hydrophobic interactions: A:F.185, A:D.211, A:V.234, A:I.343 Hydrogen bonds: A:S.267 Water bridges: A:Y.180, A:H.183, A:D.211, A:D.211, A:R.303 7T7.5: 16 residues within 4Å: Chain A: D.8, Y.10 Chain B: Y.180, H.183, F.185, R.188, D.211, V.234, A.236, P.265, S.267, I.301, R.303, I.343, A.371 Ligands: SO4.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.180, B:F.185, B:D.211, B:V.234, B:I.343 Hydrogen bonds: B:S.267 Water bridges: B:Y.180, B:D.211, B:D.211, B:R.303 pi-Stacking: B:F.185, A:Y.10

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: R.188, E.238, H.239, R.303, D.305 Chain B: Y.10 Ligands: 7T7.1, SO4.6 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:Y.10, A:H.239 Water bridges: A:R.188, A:S.240, A:R.303, A:R.303 Salt bridges: A:R.188, A:H.239, A:R.303 SO4.3: 4 residues within 4Å: Chain A: R.384, S.390, K.392, K.407 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.390, A:S.390, B:R.188 Water bridges: A:R.384, A:R.384, A:K.392 Salt bridges: A:R.384, A:K.392, A:K.407 SO4.4: 4 residues within 4Å: Chain A: R.384 Chain B: G.189, G.375, G.376 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.376 Water bridges: B:G.189, B:G.377, A:R.384, A:D.385 Salt bridges: A:R.384 SO4.6: 7 residues within 4Å: Chain A: R.188 Chain B: R.32, R.384, S.390, K.392, K.407 Ligands: SO4.2 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.390, A:R.188 Water bridges: B:R.384, B:R.384, B:K.407, B:K.407 Salt bridges: B:R.32, B:R.384, B:K.392, B:K.407 SO4.7: 5 residues within 4Å: Chain A: G.189, G.375, G.376 Chain B: R.384, D.385 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.376 Water bridges: A:G.375, A:G.377, B:R.384 Salt bridges: B:R.384 SO4.8: 7 residues within 4Å: Chain A: Y.10 Chain B: R.188, E.238, H.239, R.303, D.305 Ligands: 7T7.5 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.239 Water bridges: B:R.188, B:R.188, B:S.240, A:Y.10, A:K.392, A:K.392, A:K.392 Salt bridges: B:R.188, B:H.239, B:R.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilsbacher, J.L. et al., Discovery and Characterization of Novel Nonsubstrate and Substrate NAMPT Inhibitors. Mol. Cancer Ther. (2017)

Release Date

2017-06-28

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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