SMTL ID : 3nj4.1

Fluoro-neplanocin A in Human S-Adenosylhomocysteine Hydrolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 32 residues within 4Å: Chain A: T.160, T.161, T.162, D.193, N.194, G.223, Y.224, G.225, D.226, V.227, T.245, E.246, I.247, D.248, N.251, T.278, T.279, G.280, C.281, I.284, I.302, G.303, H.304, L.347, N.349, H.356 Chain B: L.412, Q.416, L.420, K.429, Y.433 Ligands: AFX.2 28 PLIP interactions: 23 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.194, A:V.227 Hydrogen bonds: A:T.160, A:T.161, A:T.161, A:T.161, A:T.162, A:T.162, A:Y.224, A:D.226, A:V.227, A:I.247, A:D.248, A:T.279, A:T.279, A:I.302, A:H.304, A:N.349, B:Q.416, B:Q.416, B:K.429, B:K.429 Water bridges: A:D.226, A:D.226, A:G.228, A:G.228, A:T.245 Salt bridges: B:K.429 NAD.3: 31 residues within 4Å: Chain A: Q.416, L.420, K.429, Y.433 Chain B: T.160, T.161, T.162, D.193, N.194, C.198, G.223, Y.224, G.225, D.226, V.227, T.245, E.246, I.247, D.248, N.251, T.278, T.279, C.281, I.284, I.302, G.303, H.304, L.347, N.349, H.356 Ligands: AFX.4 23 PLIP interactions: 5 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:Q.416, A:K.429, A:K.429, A:Y.433, B:T.161, B:T.161, B:T.162, B:T.162, B:T.162, B:Y.224, B:D.226, B:V.227, B:I.247, B:D.248, B:I.302, B:H.304, B:N.349 Salt bridges: A:K.429 Hydrophobic interactions: B:V.227 Water bridges: B:G.225, B:G.225, B:G.303, B:F.305 NAD.5: 32 residues within 4Å: Chain C: T.160, T.161, T.162, D.193, N.194, G.223, Y.224, G.225, D.226, V.227, T.245, E.246, I.247, D.248, N.251, T.278, T.279, G.280, C.281, I.284, I.302, G.303, H.304, L.347, N.349, H.356 Chain D: L.412, Q.416, L.420, K.429, Y.433 Ligands: AFX.6 22 PLIP interactions: 18 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:V.227 Hydrogen bonds: C:T.161, C:T.161, C:T.162, C:T.162, C:T.162, C:D.226, C:V.227, C:I.247, C:D.248, C:N.251, C:I.302, C:H.304, C:N.349, D:Q.416, D:K.429, D:K.429 Water bridges: C:D.226, C:D.226, C:T.279, C:E.308 Salt bridges: D:K.429 NAD.7: 33 residues within 4Å: Chain C: L.412, Q.416, L.420, K.429, Y.433 Chain D: T.160, T.161, T.162, D.193, N.194, C.198, G.223, Y.224, G.225, D.226, V.227, T.245, E.246, I.247, D.248, N.251, T.278, T.279, G.280, C.281, I.284, I.302, G.303, H.304, L.347, N.349, H.356 Ligands: AFX.8 25 PLIP interactions: 6 interactions with chain C, 19 interactions with chain D Hydrogen bonds: C:Q.416, C:K.429, C:K.429, C:Y.433, D:T.160, D:T.161, D:T.162, D:T.162, D:N.194, D:D.226, D:V.227, D:I.247, D:D.248, D:N.251, D:I.302, D:H.304, D:N.349 Water bridges: C:Q.416, D:G.225, D:G.228, D:F.305, D:E.308 Salt bridges: C:K.429 Hydrophobic interactions: D:N.194, D:V.227

4 x AFX: (4S,5S)-4-(6-amino-9H-purin-9-yl)-3-fluoro-5-hydroxy-2-(hydroxymethyl)cyclopent-2-en-1-one(Non-covalent)

AFX.2: 20 residues within 4Å: Chain A: L.57, H.58, T.60, E.62, T.63, D.134, E.159, T.160, K.189, D.193, H.304, L.347, N.349, L.350, M.354, G.355, H.356, M.361, F.365 Ligands: NAD.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.60, A:E.62, A:T.160, A:K.189, A:H.304, A:H.356 AFX.4: 19 residues within 4Å: Chain B: L.57, H.58, T.60, E.62, T.63, D.134, E.159, T.160, K.189, D.193, H.304, L.347, L.350, M.354, G.355, H.356, M.361, F.365 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.62, B:E.62, B:T.160, B:K.189, B:H.304, B:H.356 AFX.6: 18 residues within 4Å: Chain C: H.58, T.60, E.62, T.63, D.134, E.159, T.160, K.189, D.193, H.304, L.347, L.350, M.354, G.355, H.356, M.361, F.365 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.62, C:E.159, C:T.160, C:K.189, C:H.304, C:G.355, C:H.356 AFX.8: 19 residues within 4Å: Chain D: L.57, H.58, T.60, E.62, T.63, D.134, E.159, T.160, K.189, D.193, H.304, L.347, L.350, M.354, G.355, H.356, M.361, F.365 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.60, D:E.159, D:T.160, D:K.189, D:H.304, D:G.355, D:H.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, K.M. et al., X-ray crystal structure and binding mode analysis of human S-adenosylhomocysteine hydrolase complexed with novel mechanism-based inhibitors, haloneplanocin A analogues. J.Med.Chem. (2011)

Release Date

2011-05-04

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Adenosylhomocysteinase