- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x 2HL: 1-[(1-benzoylpiperidin-4-yl)methyl]-N-(pyridin-3-yl)-1H-benzimidazole-5-carboxamide(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.2: 6 residues within 4Å:- Chain A: R.40, R.392, S.398, K.400, K.415
- Ligands: EDO.19
14 PLIP interactions:14 interactions with chain A- Hydrogen bonds: A:S.398, A:S.398, A:S.398
- Water bridges: A:R.392, A:D.393, A:C.397, A:F.399, A:K.400, A:K.400, A:K.415
- Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415
PO4.18: 5 residues within 4Å:- Chain B: R.40, R.392, S.398, K.400, K.415
15 PLIP interactions:12 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:S.398, B:S.398
- Water bridges: B:R.40, B:R.392, B:D.393, B:F.399, B:K.400, B:K.400, A:D.313, A:D.313, A:D.354
- Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 8 residues within 4Å:- Chain A: K.400, C.401, F.414, K.415, S.425
- Chain B: H.247, S.248, T.251
Ligand excluded by PLIPEDO.4: 3 residues within 4Å:- Chain A: K.77, E.98, N.102
Ligand excluded by PLIPEDO.5: 6 residues within 4Å:- Chain A: S.31, K.32, N.136, T.137, D.138, P.139
Ligand excluded by PLIPEDO.6: 3 residues within 4Å:- Chain A: G.315, D.354, G.355
Ligand excluded by PLIPEDO.7: 8 residues within 4Å:- Chain A: H.247, S.248, T.251
- Chain B: K.400, C.401, F.414, K.415, S.425
Ligand excluded by PLIPEDO.8: 5 residues within 4Å:- Chain A: F.123, V.124, R.434, N.479
- Ligands: EDO.11
Ligand excluded by PLIPEDO.9: 6 residues within 4Å:- Chain A: K.169, E.187, V.213, N.214, K.216, R.477
Ligand excluded by PLIPEDO.10: 4 residues within 4Å:- Chain A: N.67, K.71, K.229, Y.230
Ligand excluded by PLIPEDO.11: 5 residues within 4Å:- Chain A: E.56, V.124, R.166, N.483
- Ligands: EDO.8
Ligand excluded by PLIPEDO.12: 1 residues within 4Å:- Chain A: K.24
Ligand excluded by PLIPEDO.13: 6 residues within 4Å:- Chain A: F.9, N.10, L.13, A.14
- Chain B: Y.195, A.222
Ligand excluded by PLIPEDO.14: 3 residues within 4Å:- Chain A: K.42, D.393, N.396
Ligand excluded by PLIPEDO.19: 5 residues within 4Å:- Chain A: K.423
- Chain B: D.313, G.353, D.354
- Ligands: PO4.2
Ligand excluded by PLIPEDO.20: 5 residues within 4Å:- Chain B: P.120, F.123, Y.471, N.479
- Ligands: EDO.23
Ligand excluded by PLIPEDO.21: 6 residues within 4Å:- Chain B: S.31, K.32, N.136, T.137, D.138, P.139
Ligand excluded by PLIPEDO.22: 4 residues within 4Å:- Chain B: N.67, K.71, K.229, Y.230
Ligand excluded by PLIPEDO.23: 5 residues within 4Å:- Chain B: S.470, Y.471, S.472, E.475
- Ligands: EDO.20
Ligand excluded by PLIPEDO.24: 7 residues within 4Å:- Chain B: K.169, E.187, V.213, N.214, F.215, K.216, R.477
Ligand excluded by PLIPEDO.25: 4 residues within 4Å:- Chain B: S.180, G.181, N.182, S.338
Ligand excluded by PLIPEDO.26: 4 residues within 4Å:- Chain B: A.225, L.226, K.229, Y.230
Ligand excluded by PLIP- 2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)
DTT.15: 8 residues within 4Å:- Chain A: R.392, D.393
- Chain B: F.193, G.194, R.196, G.197, G.383, G.384
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:R.392, A:D.393, A:D.393, B:G.384
- Water bridges: A:R.392, A:R.392
DTT.16: 8 residues within 4Å:- Chain A: F.193, R.196, G.197, G.353, G.355, G.383, G.384
- Chain B: R.392
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:R.392, A:G.384
- Water bridges: A:G.385
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dragovich, P.S. et al., Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg.Med.Chem.Lett. (2014)
- Release Date
- 2014-02-19
- Peptides
- Nicotinamide phosphoribosyltransferase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.72 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x 2HL: 1-[(1-benzoylpiperidin-4-yl)methyl]-N-(pyridin-3-yl)-1H-benzimidazole-5-carboxamide(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dragovich, P.S. et al., Fragment-based design of 3-aminopyridine-derived amides as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg.Med.Chem.Lett. (2014)
- Release Date
- 2014-02-19
- Peptides
- Nicotinamide phosphoribosyltransferase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B