SMTL ID : 6atb.2 (1 other biounit)

Crystal Structure of human NAMPT in complex with NVP-LOD812

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: D.85, V.86, E.89 Chain B: K.228, P.236, V.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.228

2 x BWA: N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-N'-[(pyridin-3-yl)methyl]urea(Non-covalent)

BWA.2: 15 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: Y.18 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.193, A:V.242, A:P.273, A:P.307, A:I.309, A:I.351 Hydrogen bonds: A:R.196, A:S.275 Water bridges: A:D.219, A:V.242, A:R.311 pi-Stacking: A:F.193, B:Y.18 BWA.7: 16 residues within 4Å: Chain A: 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, R.349, I.351, A.379 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.219, B:V.242, B:P.273, B:P.307, B:I.309, B:R.349, B:I.351 Hydrogen bonds: B:S.275 Water bridges: B:D.219, B:V.242 pi-Stacking: B:F.193, A:Y.18

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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:V.124, A:R.434 Water bridges: A:V.124 GOL.4: 8 residues within 4Å: Chain A: F.9, N.10, L.13, A.14 Chain B: Y.195, Q.201, A.222, A.225 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.195, B:Q.201, A:N.10 Water bridges: B:L.226 GOL.8: 5 residues within 4Å: Chain B: F.123, V.124, R.434, F.440, N.479 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.124, B:R.434, B:R.434

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

PO4.5: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.392, A:R.392, A:S.398, A:F.399, A:K.400, B:R.196 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.423 PO4.6: 5 residues within 4Å: Chain B: R.40, R.392, S.398, K.400, K.423 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Water bridges: B:R.40, B:R.392, B:D.393, B:K.400, B:K.400, B:K.400, B:K.400, B:K.423, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400

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

2018-09-12

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Nicotinamide phosphoribosyltransferase

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