SMTL ID : 8dsc.1

Human NAMPT in complex with substrate NAM and small molecule activator NP-A1-R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

homo-dimer

Ligands

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.1: 7 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311 Chain B: D.16, Y.18 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.8: 7 residues within 4Å: Chain A: D.16, Y.18 Chain B: F.193, R.196, D.219, A.244, R.311 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B pi-Stacking: A:Y.18, B:F.193 Hydrophobic interactions: B:F.193, B:D.219 Hydrogen bonds: B:D.219

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

PO4.2: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398 Water bridges: A:R.40, A:R.392, A:R.392, A:N.396, A:K.400, A:K.400, A:K.400, A:K.400, A:K.415, A:K.415, A:K.423, B:D.354 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.9: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400, K.423 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:C.397 Water bridges: B:R.40, B:R.392, B:N.396, B:K.400, B:K.400, B:K.400, B:K.415, B:K.423 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415

2 x TIE: (3R)-1-[2-(4-methylphenyl)-2H-pyrazolo[3,4-d]pyrimidin-4-yl]-N-{[4-(methylsulfanyl)phenyl]methyl}piperidine-3-carboxamide(Non-covalent)

TIE.3: 13 residues within 4Å: Chain A: G.185, Y.188, K.189, H.191, V.242, P.273, T.304, P.307, I.309, R.349, V.350, I.351, A.379 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.188, A:V.242, A:P.307, A:I.309, A:R.349, A:A.379 Hydrogen bonds: A:K.189 Water bridges: A:T.304 TIE.10: 14 residues within 4Å: Chain B: G.185, Y.188, K.189, H.191, V.242, P.273, T.304, P.307, I.309, R.349, V.350, I.351, I.378, A.379 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.188, B:V.242, B:P.307, B:I.309, B:R.349, B:A.379 Hydrogen bonds: B:K.189 Water bridges: B:T.304

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: G.122, F.123, V.124, R.434, F.440, N.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.124, A:R.434 Water bridges: A:N.479 GOL.11: 3 residues within 4Å: Chain B: K.469, S.470, Y.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.469, B:S.470, B:S.470 Water bridges: B:T.468 GOL.12: 5 residues within 4Å: Chain B: G.122, F.123, V.124, F.440, N.479 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.124, B:R.434

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

CL.5: 3 residues within 4Å: Chain A: Y.18 Chain B: E.246, R.311 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: 4 residues within 4Å: Chain A: K.73, T.76, K.77, L.105 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 4 residues within 4Å: Chain B: K.73, T.76, K.77, L.105 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.73, B:K.73, B:K.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ratia, K.M. et al., Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular NAD. Biochemistry (2023)

Release Date

2023-03-08

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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