SMTL ID : 7ppi.2 (1 other biounit)

Crystal STRUCTURE OF NAMPT IN COMPLEX WITH Compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

2 x 7Z2: N-[4-[(5R)-1-(4-azanylbutyl)-6-oxidanylidene-5-quinolin-5-yl-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide(Non-covalent)

7Z2.1: 22 residues within 4Å: Chain A: G.186, Y.189, K.190, H.192, F.194, R.197, D.220, Y.241, S.242, V.243, A.245, S.276, I.310, R.312, R.350, V.351, I.352, E.377, N.378, I.379, A.380 Chain B: Y.19 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.189, A:D.220, A:V.243, A:I.310, A:I.310, A:R.350, A:I.352, A:A.380 Hydrogen bonds: A:K.190, 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 7Z2.8: 23 residues within 4Å: Chain A: Y.19 Chain B: G.186, Y.189, K.190, H.192, F.194, R.197, D.220, Y.241, S.242, V.243, A.245, P.274, S.276, I.310, R.312, R.350, V.351, I.352, E.377, N.378, I.379, A.380 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.189, B:D.220, B:V.243, B:I.310, B:I.310, B:R.350, B:I.352, B:A.380 Hydrogen bonds: B:Y.189, B:K.190, B:S.276 Water bridges: B:D.220, B:D.220 pi-Stacking: B:F.194, A:Y.19

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

PO4.2: 6 residues within 4Å: Chain A: R.41, R.393, C.398, S.399, K.401, K.416 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.399, A:S.399, A:S.399 Water bridges: A:R.393 Salt bridges: A:R.41, A:R.393, A:K.401, A:K.416, A:K.424 PO4.9: 5 residues within 4Å: Chain B: R.41, R.393, S.399, K.401, K.416 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Water bridges: B:R.393, B:R.393, B:R.393, B:F.400, B:F.400, B:K.416, B:K.416, B:K.424, A:D.355 Salt bridges: B:R.41, B:R.393, B:K.401, B:K.416

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

CL.3: 4 residues within 4Å: Chain A: E.247, H.248, R.312 Chain B: Y.19 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: Y.19 Chain B: E.247, H.248, R.312 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: G.384, G.385 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: F.124, V.125, R.435, N.480 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.125, A:R.435, A:R.435 Water bridges: A:N.480 GOL.7: 3 residues within 4Å: Chain A: F.97, E.99, K.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.97, A:E.99, A:E.99

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
C

B
D

Nicotinamide phosphoribosyltransferase

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