SMTL ID : 9jwj.1

Structure of Human HDAC2 in complex with inhibitor N-(2-amino-5-(furan-2-yl)phenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265 ZN.13: 4 residues within 4Å: Chain B: D.177, H.179, D.265 Ligands: 01.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.177, B:D.177, B:H.179, B:D.265 ZN.23: 4 residues within 4Å: Chain C: D.177, H.179, D.265 Ligands: 01.26 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.177, C:H.179, C:D.265

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.2, H2O.4 CA.14: 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.15: 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.14, H2O.16 CA.24: 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.25: 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.24, H2O.26

3 x 01: N-(2-amino-5-(furan-2-yl)phenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamid

01.4: 22 residues within 4Å: Chain A: Y.25, M.31, R.35, 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.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.140, A:F.151, 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 01.16: 21 residues within 4Å: Chain B: Y.25, M.31, R.35, 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.13 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.140, B:L.140, B:F.151, B:F.206, B:F.206, B:L.272 Hydrogen bonds: B:G.150, B:D.177, B:H.179, B:D.265, B:Y.304 pi-Stacking: B:F.151 01.26: 21 residues within 4Å: Chain C: Y.25, M.31, R.35, 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.23 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.140, C:F.151, C:F.206, C:F.206, C:L.272 Hydrogen bonds: C:H.142, C:G.150 pi-Stacking: C:F.151

9 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: 3 residues within 4Å: Chain A: L.165, Q.169, R.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.169, A:R.193, A:R.193 EDO.7: 4 residues within 4Å: Chain A: Q.128, Q.129, T.130, D.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.129 EDO.8: 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:S.237, A:E.361, A:E.361 EDO.17: 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:G.339 Water bridges: B:R.307 EDO.18: 4 residues within 4Å: Chain B: R.170, M.252, Y.253, Q.254 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.252 EDO.19: 3 residues within 4Å: Chain B: P.30, D.100, F.151 No protein-ligand interaction detected (PLIP) EDO.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 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.9: 4 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.19, A:N.22 PEG.10: 5 residues within 4Å: Chain A: H.29, P.30, D.100, L.272 Ligands: 01.4 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain A: N.22, Y.24, H.34, R.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.34 PEG.21: 3 residues within 4Å: Chain B: Y.24, H.34, R.37 No protein-ligand interaction detected (PLIP) PEG.29: 5 residues within 4Å: Chain B: P.340, D.341 Chain C: L.162, A.187, F.188 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.193

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

PGE.12: 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

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

PG4.22: 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 PG4.30: 6 residues within 4Å: Chain B: N.350 Chain C: L.165, K.166, Y.167, Q.169, R.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.350

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.28: 6 residues within 4Å: Chain B: K.280, N.327, H.345 Chain C: E.63, T.66, K.67 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.280, C:T.66, C:T.66 Water bridges: B:N.327

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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