Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4LY1

Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004407	molecular_function	histone deacetylase activity
B	0004407	molecular_function	histone deacetylase activity
C	0004407	molecular_function	histone deacetylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 401

Chain	Residue
A	ASP181
A	HIS183
A	ASP269
A	20Y407

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA A 402

Chain	Residue
A	ASP179
A	ASP181
A	HIS183
A	SER202
A	PHE203

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA A 403

Chain	Residue
A	PHE192
A	THR195
A	VAL198
A	TYR227
A	HOH520
A	HOH521

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PG4 A 404

Chain	Residue
A	LYS71
A	ALA191
A	PHE192

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PG4 A 405

Chain	Residue
A	ARG311
A	GLU340
A	TYR341
A	GLY343
A	HOH791

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PG4 A 406

Chain	Residue
A	ASP23
A	ASN26
A	TYR27

site_id	AC7
Number of Residues	20
Details	BINDING SITE FOR RESIDUE 20Y A 407

Chain	Residue
A	TYR29
A	MET35
A	ARG39
A	GLY143
A	LEU144
A	HIS145
A	HIS146
A	GLY154
A	PHE155
A	CYS156
A	ASP181
A	HIS183
A	PHE210
A	ASP269
A	LEU276
A	GLY305
A	GLY306
A	TYR308
A	ZN401
A	HOH593

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 401

Chain	Residue
B	ASP181
B	HIS183
B	ASP269
B	20Y408

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA B 402

Chain	Residue
B	ASP179
B	ASP181
B	HIS183
B	SER202
B	PHE203

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 403

Chain	Residue
B	PHE192
B	THR195
B	VAL198
B	TYR227
B	HOH514
B	HOH535

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NHE B 404

Chain	Residue
A	TYR59
A	LYS128
A	HOH583
B	ASP21
B	ASP23
B	TYR27
B	ARG60
B	LYS63
B	GLU113
B	PG4407

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PG4 B 405

Chain	Residue
A	HOH783
B	ARG311
B	GLU340
B	TYR341
B	GLY343
B	HOH714

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PG4 B 406

Chain	Residue
B	LYS284
B	GLU328
B	ASN331
B	HIS349
C	GLU67
C	THR70

site_id	BC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PG4 B 407

Chain	Residue
A	ARG131
A	HOH631
B	ASP23
B	ASN26
B	TYR27
B	ASP109
B	NHE404
B	HOH736
B	HOH748
B	HOH822

site_id	BC6
Number of Residues	21
Details	BINDING SITE FOR RESIDUE 20Y B 408

Chain	Residue
B	HIS146
B	GLY154
B	PHE155
B	CYS156
B	ASP181
B	HIS183
B	PHE210
B	ASP269
B	GLY305
B	GLY306
B	TYR308
B	ZN401
B	HOH602
B	HOH617
B	HOH639
B	TYR29
B	MET35
B	ARG39
B	GLY143
B	LEU144
B	HIS145

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 401

Chain	Residue
C	ASP181
C	HIS183
C	ASP269
C	20Y406

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA C 402

Chain	Residue
C	ASP179
C	ASP181
C	HIS183
C	SER202
C	PHE203

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA C 403

Chain	Residue
C	PHE192
C	THR195
C	VAL198
C	TYR227
C	HOH501
C	HOH503

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PG4 C 404

Chain	Residue
B	ASP345
C	ALA191
C	ARG197
C	HOH558
C	HOH576

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PG4 C 405

Chain	Residue
B	ASN354
C	LEU169
C	LYS170
C	TYR171
C	GLN173
C	ARG197
C	HOH687

site_id	CC3
Number of Residues	20
Details	BINDING SITE FOR RESIDUE 20Y C 406

Chain	Residue
C	TYR29
C	MET35
C	ARG39
C	GLY143
C	LEU144
C	HIS145
C	HIS146
C	GLY154
C	PHE155
C	CYS156
C	ASP181
C	HIS183
C	PHE210
C	ASP269
C	GLY305
C	GLY306
C	TYR308
C	ZN401
C	HOH583
C	HOH586

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	939
Details	Region: {"description":"Histone deacetylase"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	3
Details	Active site: {"evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"O15379","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	27
Details	Binding site: {"evidences":[{"source":"PubMed","id":"37137925","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8BPA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"37137925","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8BPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	6
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P70288","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)