SMTL ID : 6b76.1 (1 other biounit)

Crystal Structure of human NAMPT in complex with NVP-LVR596

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

2 x CVJ: (1S,2S)-N-{4-[(1S)-1-(propanoylamino)ethyl]phenyl}-2-(pyridin-3-yl)cyclopropane-1-carboxamide(Non-covalent)

CVJ.1: 17 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, A.245, S.275, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.188, A:F.193, A:D.219, A:Y.240, A:V.242, A:A.244, A:I.309, A:I.351, A:A.379, B:Y.18 Hydrogen bonds: A:S.275 Water bridges: A:Y.188, A:D.219, A:S.241 pi-Stacking: A:F.193, B:Y.18 CVJ.5: 17 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, Y.240, S.241, V.242, A.244, A.245, S.275, I.309, R.311, I.351, A.379 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.188, B:F.193, B:D.219, B:Y.240, B:V.242, B:A.244, B:I.309, B:I.351, B:A.379, A:Y.18 Hydrogen bonds: B:S.275 Water bridges: B:Y.188, B:H.191, B:D.219, B:D.219 pi-Stacking: B:F.193, A:Y.18

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

PO4.2: 7 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 Ligands: PO4.7 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.40, A:R.392, A:K.400, A:K.415, A:K.415, A:K.415, A:K.415 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.3: 7 residues within 4Å: Chain A: R.196, A.245, E.246, H.247, R.311, D.313 Chain B: Y.18 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.245, A:H.247 Water bridges: A:R.196, A:R.196, A:R.196, A:S.248, B:E.149, B:E.149, B:K.400 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.4: 6 residues within 4Å: Chain A: G.353, G.355, G.383, G.384 Chain B: R.392 Ligands: PO4.8 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.355, A:G.383, A:G.384, B:R.392 Water bridges: A:G.353, A:D.354, A:V.356, A:V.356, A:V.356, A:S.382 PO4.6: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, A.245, E.246, H.247, R.311, D.313 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.245, B:H.247, A:Y.18, A:Y.18 Water bridges: B:R.196, B:R.196, B:R.196, B:H.247, B:S.248, A:K.400, A:K.400 Salt bridges: B:R.196, B:H.247, B:R.311 PO4.7: 6 residues within 4Å: Chain A: R.392 Chain B: G.353, G.355, G.383, G.384 Ligands: PO4.2 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.355, B:G.383, B:G.384, A:R.392 Water bridges: B:D.354, B:D.354, B:G.385, A:D.393, A:D.393 PO4.8: 7 residues within 4Å: Chain B: R.40, R.392, S.398, K.400, K.415, K.423 Ligands: PO4.4 15 PLIP interactions: 15 interactions with chain B Water bridges: B:R.40, B:R.392, B:R.392, B:R.392, B:F.399, B:K.400, B:K.415, B:K.415, B:K.415, B:K.423 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palacios, D. et al., Identification and structure based design of cellularly active cyclo-propyl carboxamide Nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. To Be Published

Release Date

2018-10-03

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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