SMTL ID : 5nsd.1

Co-crystal structure of NAMPT dimer with KPT-9274

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400 Ligands: GOL.13 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Water bridges: B:D.313, A:R.392, A:K.400, A:K.400 Hydrogen bonds: A:S.398 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.423 PO4.12: 5 residues within 4Å: Chain B: R.40, R.392, S.398, K.400 Ligands: GOL.2 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.398 Water bridges: B:R.40, B:R.40, B:R.392, B:K.400, B:K.415, A:D.313 Salt bridges: B:R.40, B:R.392, B:K.400

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: D.313, G.353, D.354 Chain B: K.423 Ligands: 96Q.11, PO4.12 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.313, A:D.354, B:K.423 Water bridges: A:R.311, A:D.313, A:D.313, A:D.354, A:G.355 GOL.3: 5 residues within 4Å: Chain A: F.123, V.124, R.434, F.440, N.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.124, A:R.434, A:N.479 GOL.4: 2 residues within 4Å: Chain A: V.300, Y.347 No protein-ligand interaction detected (PLIP) GOL.5: 6 residues within 4Å: Chain A: R.40, D.393, N.396, D.420, K.423 Ligands: GOL.13 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.40, A:N.396, A:K.423 Water bridges: A:D.420, B:D.354 GOL.6: 8 residues within 4Å: Chain A: F.9, N.10, L.13, A.14 Chain B: Y.195, Q.201, A.222, A.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.195, B:Q.201 Water bridges: B:A.222 GOL.7: 6 residues within 4Å: Chain A: Y.54, N.164, I.358, G.385, K.389, L.390 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.385 Water bridges: A:N.164, A:I.358 GOL.8: 5 residues within 4Å: Chain A: Y.64, K.68, E.202, L.226, Y.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.64 Water bridges: A:K.68, A:K.68, A:K.68 GOL.9: 8 residues within 4Å: Chain A: Y.240, S.241, V.242, P.273 Chain B: H.90, F.91, Q.92 Ligands: 96Q.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.90, A:S.241 GOL.10: 1 residues within 4Å: Chain A: E.187 No protein-ligand interaction detected (PLIP) GOL.13: 6 residues within 4Å: Chain A: K.423 Chain B: D.313, G.353, D.354 Ligands: PO4.1, GOL.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.313, B:G.353, A:K.423 GOL.14: 5 residues within 4Å: Chain B: Q.63, Y.230, Y.231, S.470, Y.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.63, B:Y.230, B:S.470 Water bridges: B:S.470 GOL.15: 4 residues within 4Å: Chain B: K.469, Y.471, E.475, N.479 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.479 Water bridges: B:S.470, B:S.470, B:E.475 GOL.16: 5 residues within 4Å: Chain B: F.123, V.124, R.434, F.440, N.479 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.124, B:R.434, B:R.434, B:N.479 GOL.17: 8 residues within 4Å: Chain B: K.169, E.187, L.212, V.213, N.214, F.215, K.216, R.477 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.187, B:V.213, B:F.215 Water bridges: B:N.214

2 x 96Q: (~{E})-3-(6-azanylpyridin-3-yl)-~{N}-[[5-[4-[4,4-bis(fluoranyl)piperidin-1-yl]carbonylphenyl]-7-(4-fluorophenyl)-1-benzofuran-2-yl]methyl]prop-2-enamide(Non-covalent)

96Q.11: 22 residues within 4Å: Chain A: E.187, Y.188, H.191, F.193, R.196, K.216, G.217, D.219, Y.240, S.241, V.242, A.244, S.275, I.309, R.311, R.349, A.379 Chain B: D.16, Y.18, Q.92 Ligands: GOL.2, GOL.9 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.188, A:Y.188, A:F.193, A:K.216, A:Y.240, A:V.242, A:V.242, A:I.309, A:I.309, A:A.379, B:Y.18 Hydrogen bonds: A:S.275, B:D.16 Water bridges: A:R.196, A:D.219, A:S.241, A:A.245 pi-Stacking: A:F.193 Halogen bonds: B:Q.92 96Q.18: 17 residues within 4Å: Chain A: Y.18, Q.92 Chain B: Y.188, H.191, F.193, R.196, K.216, G.217, D.219, Y.240, V.242, A.244, S.275, I.309, R.311, R.349, A.379 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.188, B:Y.188, B:F.193, B:K.216, B:Y.240, B:V.242, B:I.309, B:A.379, A:Y.18, A:Q.92 Hydrogen bonds: B:R.196, B:S.275, A:Y.18 Water bridges: B:R.196, B:A.245, B:R.311 pi-Stacking: B:F.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neggers, J.E. et al., Target identification of small molecules using large-scale CRISPR-Cas mutagenesis scanning of essential genes. Nat Commun (2018)

Release Date

2018-02-14

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase