SMTL ID : 9k0g.1

Structure of Human HDAC2 in complex with inhibitor N-(2-aminophenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: 01.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265, 01.4 ZN.12: 4 residues within 4Å: Chain B: D.177, H.179, D.265 Ligands: 01.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.177, B:D.177, B:H.179, B:D.265, 01.15 ZN.22: 4 residues within 4Å: Chain C: D.177, H.179, D.265 Ligands: 01.25 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.177, C:D.177, C:H.179, C:D.265, 01.25

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:D.175, A:D.177, A:H.179, A:S.198 CA.3: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:T.191, A:V.194, H2O.3, H2O.5 CA.13: 6 residues within 4Å: Chain B: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.175, B:D.175, B:D.177, B:H.179, B:S.198 CA.14: 4 residues within 4Å: Chain B: F.188, T.191, V.194, Y.223 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.188, B:T.191, B:V.194, H2O.16, H2O.18 CA.23: 6 residues within 4Å: Chain C: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.175, C:D.175, C:D.177, C:H.179, C:S.198 CA.24: 4 residues within 4Å: Chain C: F.188, T.191, V.194, Y.223 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:F.188, C:T.191, C:V.194, H2O.27, H2O.29

3 x 01: N-(2-aminophenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamide

01.4: 20 residues within 4Å: Chain A: M.31, D.100, G.139, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.206, Q.261, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.1, PEG.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.140, A:F.206, A:F.206, A:L.272 Hydrogen bonds: A:H.142, A:G.150, A:Y.304 pi-Stacking: A:F.151 01.15: 19 residues within 4Å: Chain B: M.31, D.100, G.139, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.206, Q.261, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.140, B:F.206, B:F.206, B:L.272 Hydrogen bonds: B:H.142, B:G.150, B:Y.304 pi-Stacking: B:F.151 01.25: 19 residues within 4Å: Chain C: M.31, D.100, G.139, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.206, Q.261, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.22 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.140, C:F.206, C:L.272 Hydrogen bonds: C:H.142, C:G.150 pi-Stacking: C:F.151

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

EDO.5: 2 residues within 4Å: Chain A: A.187, F.188 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: L.165, K.166, Y.167, Q.169, R.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.193 Water bridges: A:R.193 EDO.7: 5 residues within 4Å: Chain A: S.237, Q.240, P.357, M.360, E.361 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.361, A:E.361 Water bridges: A:T.356 EDO.16: 4 residues within 4Å: Chain B: R.307, E.336, Y.337, G.339 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.307 Water bridges: B:R.307 EDO.17: 3 residues within 4Å: Chain B: R.170, M.252, Y.253 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.254 EDO.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.26: 7 residues within 4Å: Chain A: F.368, E.369, R.372 Chain C: R.94, F.95, S.146, E.147 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.146, C:E.147, A:F.368, A:E.369 EDO.27: 2 residues within 4Å: Chain C: N.22, Y.23 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.22

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 3 residues within 4Å: Chain A: D.19, N.22, Y.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.19, A:N.22 PEG.9: 6 residues within 4Å: Chain A: H.29, P.30, E.99, F.151, L.272 Ligands: 01.4 No protein-ligand interaction detected (PLIP) PEG.10: 3 residues within 4Å: Chain A: N.22, H.34, R.37 No protein-ligand interaction detected (PLIP) PEG.20: 4 residues within 4Å: Chain B: G.21, Y.24, H.34, R.37 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.337 PEG.28: 4 residues within 4Å: Chain B: D.341 Chain C: L.162, A.187, T.191 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:D.341, C:R.193

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 4 residues within 4Å: Chain A: R.307, E.336, Y.337, G.339 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.307

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 6 residues within 4Å: Chain B: K.280, N.327, H.345 Chain C: E.63, T.66, K.67 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.280, C:T.66 Water bridges: B:K.280, B:N.327, B:N.327, B:N.327

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.21: 4 residues within 4Å: Chain B: D.19, N.22, Y.23, D.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.22 PG4.29: 8 residues within 4Å: Chain B: N.350, T.352 Chain C: L.165, K.166, Y.167, H.168, Q.169, R.193 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:L.165, C:R.193 Hydrogen bonds: B:N.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tojo, T. et al., Discovery of an HDAC2-selective inhibitor based on enzyme-inhibitor binding thermodynamics and kinetics, and its potential as a therapeutic drug for neurological disorders. To Be Published

Release Date

2025-10-15

Peptides

Histone deacetylase 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Histone deacetylase 2

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