SMTL ID : 8tm7.1

Human NAMPT in complex with substrate NAM and small molecule activator NP-A3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: N.29, T.30, P.139, E.140, Y.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:E.140 Water bridges: A:N.29 GOL.2: 6 residues within 4Å: Chain A: G.122, F.123, V.124, R.434, F.440, N.479 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.124, A:R.434

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.3: 8 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311 Chain B: D.16, Y.18 Ligands: I7Q.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.193, A:D.219 Hydrogen bonds: A:D.219 pi-Stacking: A:F.193, B:Y.18 NCA.9: 8 residues within 4Å: Chain A: D.16, Y.18 Chain B: F.193, R.196, D.219, A.244, R.311 Ligands: I7Q.10 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.193 Hydrogen bonds: B:D.219 pi-Stacking: B:F.193, A:Y.18

2 x I7Q: N-{2-[(4R)-2,2-dimethyl-4-(propan-2-yl)oxan-4-yl]ethyl}-N-[(4-methoxyphenyl)methyl]furan-2-carboxamide(Non-covalent)

I7Q.4: 17 residues within 4Å: Chain A: Y.188, K.189, H.191, F.193, V.242, P.273, Q.305, P.307, I.309, R.349, V.350, I.351, E.376, N.377, I.378, A.379 Ligands: NCA.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.188, A:Y.188, A:V.242, A:P.273, A:I.309, A:I.309, A:R.349, A:I.351, A:A.379 Water bridges: A:V.242, A:S.275 I7Q.10: 16 residues within 4Å: Chain B: Y.188, K.189, H.191, V.242, P.273, Q.305, P.307, I.309, R.349, V.350, I.351, E.376, N.377, I.378, A.379 Ligands: NCA.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.188, B:Y.188, B:P.273, B:I.309, B:R.349, B:I.351, B:A.379 Water bridges: B:V.242

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: K.73, T.76, K.77 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.246, R.311 Chain B: Y.18 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Y.18 Chain B: E.246, R.311 Ligand excluded by PLIP

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

PO4.8: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.392, A:K.400, A:K.415, A:K.415 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.11: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400, K.415 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain B Water bridges: A:R.196, B:R.392, B:R.392, B:K.400, B:K.400, B:K.415 Hydrogen bonds: B:S.398, B:S.398 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

Gordon-Blake, J. et al., Nicotinamide Phosphoribosyltransferase Positive Allosteric Modulators Attenuate Neuronal Oxidative Stress. Acs Med.Chem.Lett. (2024)

Release Date

2024-06-12

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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