SMTL ID : 4yvf.1

Structure of S-adenosyl-L-homocysteine hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 28 residues within 4Å: Chain A: D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Chain B: L.409, Q.413, K.426, Y.430 Ligands: XFA.2 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.224 Hydrogen bonds: A:D.223, A:V.224, A:I.244, A:D.245, A:N.248, A:N.346, A:N.346, B:Q.413, B:K.426, B:K.426, B:Y.430 Water bridges: A:T.158, A:T.158, A:G.222, A:G.225, A:T.242, A:H.301, B:Q.413 NAI.3: 28 residues within 4Å: Chain A: L.409, Q.413, K.426, Y.430 Chain B: D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: XFA.4 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.223, B:V.224, B:I.244, B:D.245, B:H.301, B:N.346, B:N.346, A:Q.413, A:K.426, A:K.426, A:Y.430 Water bridges: B:G.222, B:G.225, B:T.242, B:D.280, A:Q.413 NAI.5: 28 residues within 4Å: Chain C: D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Chain D: L.409, Q.413, K.426, Y.430 Ligands: XFA.6 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:V.224 Hydrogen bonds: C:D.223, C:V.224, C:I.244, C:D.245, C:N.248, C:H.301, C:N.346, C:N.346, D:Q.413, D:K.426, D:K.426, D:Y.430, D:Y.430 Water bridges: C:T.158, C:G.222, C:G.225, D:Q.413 NAI.7: 28 residues within 4Å: Chain C: L.409, Q.413, K.426, Y.430 Chain D: D.190, N.191, C.195, G.220, G.222, D.223, V.224, T.242, E.243, I.244, D.245, N.248, T.275, T.276, G.277, C.278, I.281, I.299, G.300, H.301, L.344, N.346, H.353 Ligands: XFA.8 17 PLIP interactions: 10 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:D.223, D:V.224, D:I.244, D:D.245, D:N.346, D:N.346, C:Q.413, C:K.426, C:K.426, C:Y.430, C:Y.430 Water bridges: D:G.222, D:G.225, D:D.280, D:H.301, C:T.407, C:Q.413

4 x XFA: 2-{[5-chloro-2-(4-chlorophenoxy)phenyl](2-{[2-(methylamino)ethyl]amino}-2-oxoethyl)amino}-N-(1,3-dihydro-2H-isoindol-2-yl)-N-methylacetamide(Non-covalent)

XFA.2: 14 residues within 4Å: Chain A: H.55, T.57, E.59, S.83, Q.85, D.190, L.344, N.346, L.347, M.351, G.352, H.353, M.358 Ligands: NAI.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.57, A:Q.85, A:L.344, A:L.347 Hydrogen bonds: A:T.57, A:E.59, A:E.59, A:H.353 Salt bridges: A:D.190 pi-Stacking: A:H.55 XFA.4: 14 residues within 4Å: Chain B: H.55, T.57, E.59, S.83, Q.85, D.190, L.344, N.346, L.347, M.351, G.352, H.353, M.358 Ligands: NAI.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.57, B:Q.85, B:L.344, B:L.347 Hydrogen bonds: B:T.57, B:E.59, B:E.59, B:H.353 Salt bridges: B:D.190 pi-Stacking: B:H.55 XFA.6: 14 residues within 4Å: Chain C: H.55, T.57, E.59, S.83, Q.85, D.190, L.344, N.346, L.347, M.351, G.352, H.353, M.358 Ligands: NAI.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:T.57, C:Q.85, C:L.344, C:L.347 Hydrogen bonds: C:E.59, C:H.353 Salt bridges: C:D.190 pi-Stacking: C:H.55 XFA.8: 14 residues within 4Å: Chain D: H.55, T.57, E.59, S.83, Q.85, D.190, L.344, N.346, L.347, M.351, G.352, H.353, M.358 Ligands: NAI.7 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:T.57, D:Q.85, D:L.344, D:L.347 Hydrogen bonds: D:E.59, D:H.353 Salt bridges: D:D.190 pi-Stacking: D:H.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakao, A. et al., Discovery and structural analyses of S-adenosyl-L-homocysteine hydrolase inhibitors based on non-adenosine analogs. Bioorg.Med.Chem. (2015)

Release Date

2015-11-25

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Adenosylhomocysteinase

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