SMTL ID : 7ppe.1

CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH COMPOUND 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: R.41, R.393, S.399, K.401, K.416 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.399, A:S.399, A:S.399 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, A:K.416 PO4.3: 7 residues within 4Å: Chain A: R.197, E.247, H.248, R.312, D.314 Chain B: Y.19 Ligands: 7YK.2 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.248, A:D.314, B:Y.19 Water bridges: A:R.197, A:R.197, A:R.197, A:H.248, A:S.249, B:K.401, B:K.401 Salt bridges: A:R.197, A:H.248, A:R.312, B:K.401 PO4.4: 4 residues within 4Å: Chain A: G.354, G.384, G.385 Chain B: R.393 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.384, A:G.385, B:R.393 Water bridges: A:G.354, A:D.355, A:V.357, A:G.386, B:D.394, B:D.394 PO4.6: 5 residues within 4Å: Chain B: R.41, R.393, C.398, S.399, K.401 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.399 Water bridges: B:R.393, B:K.401, B:K.416, B:K.416, B:K.416, A:R.197 Salt bridges: B:R.41, B:R.393, B:K.401, B:K.416, B:K.424 PO4.8: 7 residues within 4Å: Chain A: Y.19 Chain B: R.197, E.247, H.248, R.312, D.314 Ligands: 7YK.7 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Water bridges: A:Y.19, A:K.401, A:K.401, A:K.401, A:K.401, B:R.197, B:R.197, B:S.249, B:R.312 Salt bridges: A:K.401, B:R.197, B:H.248, B:R.312 Hydrogen bonds: B:H.248 PO4.9: 5 residues within 4Å: Chain B: G.354, G.356, G.384, G.385, G.386 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.393, B:G.356, B:G.384, B:G.385, B:G.386 Water bridges: A:R.393, B:V.357, B:V.357, B:V.357

2 x 7YK: N-[4-[(4R)-4-methyl-1-(oxan-4-yl)-6-oxidanylidene-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide(Non-covalent)

7YK.2: 14 residues within 4Å: Chain A: Y.189, H.192, F.194, R.197, D.220, V.243, A.245, S.276, R.312, I.352, A.380 Chain B: D.17, Y.19 Ligands: PO4.3 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.189, A:D.220, A:V.243, A:V.243, A:I.352, A:A.380 Hydrogen bonds: A:S.276 Water bridges: A:D.220, A:D.220, A:S.242, A:R.312 pi-Stacking: A:F.194, B:Y.19 7YK.7: 15 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, I.352, A.380 Ligands: PO4.8 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain B pi-Stacking: A:Y.19, B:F.194 Hydrophobic interactions: B:Y.189, B:D.220, B:V.243, B:V.243, B:I.310, B:I.352, B:A.380 Hydrogen bonds: B:S.276 Water bridges: B:D.220, B:D.220, B:R.312

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: G.123, F.124, V.125, R.435, F.441, N.480 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.123, A:V.125, A:R.435 GOL.10: 6 residues within 4Å: Chain B: G.123, F.124, V.125, R.435, F.441, N.480 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.123, B:V.125, B:R.435, B:R.435

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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