SMTL ID : 4kfp.1

Identification of 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine-derived Ureas as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x 1R7: N-(4-{[1-(tetrahydro-2H-pyran-4-yl)piperidin-4-yl]sulfonyl}benzyl)-2H-pyrrolo[3,4-c]pyridine-2-carboxamide(Non-covalent)

1R7.1: 20 residues within 4Å: Chain A: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, P.273, S.275, Q.305, P.307, I.309, R.311, I.351, A.379 Chain B: D.16, Y.18 Ligands: PO4.2, EDO.5 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.193, A:V.242, A:P.273, A:P.307, A:I.309, A:I.351, B:Y.18 Hydrogen bonds: A:D.219 Water bridges: A:R.311 pi-Stacking: A:H.191, A:F.193, A:F.193, B:Y.18 1R7.9: 18 residues within 4Å: Chain A: D.16, Y.18 Chain B: Y.188, H.191, F.193, R.196, D.219, S.241, V.242, A.244, S.275, Q.305, P.307, I.309, R.311, I.351, A.379 Ligands: PO4.11 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.193, B:V.242, B:P.307, B:I.309, B:I.351, A:Y.18 Hydrogen bonds: B:D.219 Water bridges: B:R.311 pi-Stacking: B:H.191, B:F.193, B:F.193, A:Y.18

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

PO4.2: 7 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: 1R7.1 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:Y.18, B:Y.18, A:H.247, A:D.313 Water bridges: B:K.400, A:R.196, A:R.196, A:R.196, A:H.247, A:S.248, A:R.311 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.3: 6 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: EDO.8, PO4.11 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.398, A:S.398, A:K.415, B:R.196 Water bridges: A:R.392, A:F.399, A:K.400, A:K.423 Salt bridges: A:R.392, A:K.400 PO4.10: 5 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: EDO.13 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.196 Water bridges: A:D.313, A:D.313, A:D.354, B:E.149, B:F.399, B:F.399, B:K.400, B:K.400, B:K.415, B:K.415, B:K.423, B:K.423 Salt bridges: B:R.392, B:K.400 PO4.11: 8 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: PO4.3, 1R7.9 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.247, A:Y.18 Water bridges: B:R.196, B:R.196, B:R.196, B:S.248, B:R.311, A:K.400, A:K.400, A:K.400 Salt bridges: B:R.196, B:H.247, B:R.311

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: F.123, V.124, R.434, N.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.124, A:R.434, A:R.434, A:N.479 EDO.5: 6 residues within 4Å: Chain A: Y.188, H.191, Y.240, S.241, V.242 Ligands: 1R7.1 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.188, A:H.191, A:S.241, A:S.241 EDO.6: 7 residues within 4Å: Chain A: K.169, E.187, V.213, N.214, F.215, K.216, R.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.213 Water bridges: A:E.187 EDO.7: 8 residues within 4Å: Chain A: K.400, C.401, F.414, K.415, S.425 Chain B: H.247, S.248, T.251 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:C.401, B:T.251 Water bridges: A:N.146, A:F.399, A:C.401, A:V.413, B:E.246, B:S.248 EDO.8: 7 residues within 4Å: Chain A: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.392, A:D.393, A:D.393, A:N.396, A:S.398 EDO.12: 8 residues within 4Å: Chain A: H.247, S.248, T.251 Chain B: K.400, C.401, F.414, K.415, S.425 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.401 Water bridges: B:N.146, B:F.399, B:C.401, B:V.413, A:E.246, A:S.248 EDO.13: 7 residues within 4Å: Chain B: R.40, R.392, D.393, N.396, C.397, S.398 Ligands: PO4.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:R.392, B:D.393, B:N.396, B:S.398 Water bridges: B:K.400

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dragovich, P.S. et al., Identification of 2,3-dihydro-1H-pyrrolo[3,4-c]pyridine-derived ureas as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-08-14

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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