SMTL ID : 8dsm.1 (1 other biounit)

Human NAMPT in complex with inhibitor ZN-4-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

2 x TK0: (3S)-N-[(1-benzothiophen-5-yl)methyl]-1-[6-(4-{2-[(2E)-3-(pyridin-3-yl)prop-2-enamido]ethyl}phenyl)thieno[2,3-d]pyrimidin-4-yl]piperidine-3-carboxamide(Non-covalent)

TK0.1: 23 residues within 4Å: Chain A: D.184, G.185, Y.188, K.189, H.191, F.193, R.196, D.219, V.242, A.244, S.275, Q.305, P.307, I.309, R.311, R.349, I.351, E.376, I.378, A.379 Chain B: D.16, Y.18 Ligands: CL.3 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.188, A:F.193, A:F.193, A:F.193, A:V.242, A:A.244, A:P.307, A:I.309, A:R.349, B:Y.18 Hydrogen bonds: A:K.189, A:S.275 Water bridges: A:V.242 TK0.6: 22 residues within 4Å: Chain A: D.16, Y.18 Chain B: G.185, Y.188, K.189, H.191, F.193, R.196, D.219, V.242, A.244, S.275, Q.305, P.307, I.309, R.311, R.349, V.350, I.351, I.378, A.379 Ligands: CL.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.188, B:F.193, B:V.242, B:V.242, B:P.307, B:I.309, B:R.349, B:I.351 Hydrogen bonds: B:K.189, B:S.275, B:R.311 Water bridges: B:A.245 pi-Stacking: B:F.193, A:Y.18

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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.398, A:S.398 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415, A:K.423 PO4.7: 5 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.398 Salt bridges: B:R.40, B:R.392, B:K.400

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

CL.3: 4 residues within 4Å: Chain A: E.246, R.311 Chain B: Y.18 Ligands: TK0.1 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Y.18 Chain B: E.246, R.311 Ligands: TK0.6 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: F.9, N.10, L.13 Chain B: Y.195, Q.201, A.222, A.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ratia, K. et al., A structural mechanism for positive allosteric modulation of nicotinamide phosphoribosyltransferase to elevate cellular NAD+. To Be Published

Release Date

2023-08-02

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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