SMTL ID : 7pph.1

CRYSTAL STRUCTURE OF NAMPT IN COMPLEX WITH Compound 10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

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

7YE.1: 16 residues within 4Å: Chain A: Y.189, H.192, F.194, R.197, D.220, V.243, A.245, P.274, S.276, P.308, I.310, R.312, I.352, A.380 Chain B: Y.19 Ligands: PO4.3 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.189, A:D.220, A:V.243, A:V.243, A:P.274, A:I.310, A:I.352 Hydrogen bonds: A:Y.189, A:S.276 Water bridges: A:K.190, A:K.190, A:K.190, A:D.220, A:D.220 pi-Stacking: A:H.192, A:F.194, B:Y.19 7YE.6: 16 residues within 4Å: Chain A: Y.19 Chain B: Y.189, H.192, F.194, R.197, D.220, V.243, A.245, P.274, S.276, P.308, I.310, R.312, I.352, A.380 Ligands: PO4.8 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B pi-Stacking: A:Y.19, B:Y.189, B:H.192, B:F.194 Hydrophobic interactions: B:D.220, B:V.243, B:V.243, B:P.274, B:I.310, B:I.352 Hydrogen bonds: B:Y.189, B:S.276 Water bridges: B:K.190, B:K.190, B:H.192, B:D.220, B:D.220, B:R.312

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

PO4.2: 5 residues within 4Å: Chain A: R.41, R.393, S.399, K.401, K.416 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.399 Water bridges: A:R.393, A:R.393, A:N.397, A:C.398, A:F.400, A:K.401, A:K.401, A:K.401, A:K.416, A:K.424, A:K.424, B:D.314, B:D.314, B:D.355, B:D.355 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: 7YE.1 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:H.248, B:Y.19, B:Y.19 Water bridges: A:R.197, A:R.197, A:R.197, A:E.247, A:S.249, A:R.312, A:R.312, B:K.401, B:K.401, B:K.401 Salt bridges: A:R.197, A:H.248, A:R.312, B:K.401 PO4.7: 5 residues within 4Å: Chain B: R.41, R.393, S.399, K.401, K.416 22 PLIP interactions: 5 interactions with chain A, 17 interactions with chain B Water bridges: A:D.314, A:D.314, A:D.355, A:D.355, A:D.355, B:R.393, B:R.393, B:R.393, B:F.400, B:K.401, B:K.401, B:K.416, B:K.424, B:K.424 Hydrogen bonds: B:S.399, B:S.399, B:S.399 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: 7YE.6 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:H.248, A:Y.19 Water bridges: B:R.197, B:R.197, B:E.247, B:S.249, B:R.312, A:Y.19, A:K.401, A:K.401, A:K.401 Salt bridges: B:R.197, B:H.248, B:R.312

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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:V.125, A:R.435, A:R.435 GOL.5: 6 residues within 4Å: Chain A: G.354, D.355, G.356, G.384, G.385 Chain B: R.393 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.355, A:G.356, A:G.384, A:G.385, B:R.393 Water bridges: A:G.354, A:D.355, A:D.355, A:V.357, A:V.357, B:R.393, B:R.393 GOL.9: 5 residues within 4Å: Chain B: G.123, F.124, V.125, R.435, N.480 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.125, B:R.435, B:R.435, B:N.480 GOL.10: 6 residues within 4Å: Chain A: R.393 Chain B: G.354, D.355, G.356, G.384, G.385 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.354, B:G.356, B:G.384, B:G.385, A:R.393 Water bridges: B:V.357, A:R.393, A:D.394

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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