SMTL ID : 7ppf.1

CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH COMPOUND 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: R.41, R.393, C.398, S.399, K.401 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.393, A:F.400, A:K.401, A:K.401, A:K.416 Salt bridges: A:R.41, A:R.393, A:K.401 PO4.6: 5 residues within 4Å: Chain B: R.41, R.393, S.399, K.401, K.416 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.399, B:S.399 Water bridges: B:R.393, B:R.393, B:F.400, B:K.401, B:K.401, B:K.416, B:K.424, B:K.424 Salt bridges: B:R.41, B:R.393, B:K.401, B:K.416

2 x 7YT: N-[4-[(4R)-1,4-dimethyl-6-oxidanylidene-4,5-dihydropyridazin-3-yl]phenyl]-5,7-dihydropyrrolo[3,4-b]pyridine-6-carboxamide(Non-covalent)

7YT.2: 15 residues within 4Å: Chain A: Y.189, H.192, F.194, R.197, D.220, V.243, A.245, S.276, I.310, R.312, V.351, I.352, A.380 Chain B: D.17, Y.19 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.194, A:D.220, A:V.243, A:V.243, A:I.310, A:I.352 Hydrogen bonds: A:S.276 Water bridges: A:D.220, A:D.220, A:R.312, A:R.312 pi-Stacking: A:F.194, B:Y.19 7YT.5: 17 residues within 4Å: Chain A: D.17, Y.19 Chain B: Y.189, H.192, F.194, R.197, D.220, V.243, A.245, S.276, I.310, R.312, R.350, V.351, I.352, A.380 Ligands: EDO.8 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.194, B:D.220, B:V.243, B:V.243, B:I.352 Hydrogen bonds: B:S.276 Water bridges: B:D.220, B:D.220, B:R.312, B:R.312, B:R.312 pi-Stacking: B:H.192, B:F.194, A:Y.19

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 2 residues within 4Å: Chain A: D.394 Chain B: G.385 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.385, A:D.394 Water bridges: B:G.384 EDO.4: 4 residues within 4Å: Chain A: F.124, V.125, R.435, N.480 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.125, A:R.435, A:N.480 EDO.7: 6 residues within 4Å: Chain B: S.32, K.33, N.137, T.138, D.139, P.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.33, B:K.33 EDO.8: 3 residues within 4Å: Chain B: G.186, Y.189 Ligands: 7YT.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bohnke, N. et al., A Novel NAMPT Inhibitor-Based Antibody-Drug Conjugate Payload Class for Cancer Therapy. Bioconjug.Chem. (2022)

Release Date

2022-06-15

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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