Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6XEB

STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND E)

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	ASP177
A	HIS179
A	ASP265
A	V1P411

site_id	AC2
Number of Residues	6
Details	binding site for residue SO4 A 402

Chain	Residue
A	HOH559
A	GLU87
A	TYR88
A	LYS90
A	GLN91
A	HOH504

site_id	AC3
Number of Residues	9
Details	binding site for residue SO4 A 403

Chain	Residue
A	ARG213
A	ARG366
A	HOH502
A	HOH505
A	HOH512
A	HOH519
B	PRO330
B	TYR331
B	HOH624

site_id	AC4
Number of Residues	5
Details	binding site for residue SO4 A 404

Chain	Residue
A	SER70
A	ASP71
A	LYS145
A	HOH503
A	HOH664

site_id	AC5
Number of Residues	4
Details	binding site for residue SO4 A 405

Chain	Residue
A	THR305
A	ARG307
A	HOH602
A	HOH671

site_id	AC6
Number of Residues	5
Details	binding site for residue CA A 406

Chain	Residue
A	ASP175
A	ASP177
A	HIS179
A	SER198
A	PHE199

site_id	AC7
Number of Residues	6
Details	binding site for residue CA A 407

Chain	Residue
A	PHE188
A	THR191
A	VAL194
A	TYR223
A	HOH558
A	HOH697

site_id	AC8
Number of Residues	4
Details	binding site for residue PEG A 408

Chain	Residue
A	ASP19
A	ASN22
A	TYR23
A	ASP105

site_id	AC9
Number of Residues	4
Details	binding site for residue PEG A 409

Chain	Residue
A	ARG307
A	GLU336
A	GLY339
A	HOH585

site_id	AD1
Number of Residues	2
Details	binding site for residue PEG A 410

Chain	Residue
A	TYR24
A	HIS34

site_id	AD2
Number of Residues	19
Details	binding site for residue V1P A 411

Chain	Residue
A	GLY28
A	PRO30
A	MET31
A	ASP100
A	HIS141
A	HIS142
A	GLY150
A	PHE151
A	ASP177
A	HIS179
A	ASP265
A	LEU272
A	GLY302
A	TYR304
A	ZN401
A	HOH513
A	HOH516
A	HOH628
A	HOH646

site_id	AD3
Number of Residues	4
Details	binding site for residue ZN B 401

Chain	Residue
B	ASP177
B	HIS179
B	ASP265
B	V1P408

site_id	AD4
Number of Residues	6
Details	binding site for residue SO4 B 402

Chain	Residue
B	GLU87
B	TYR88
B	LYS90
B	GLN91
B	HOH523
B	HOH716

site_id	AD5
Number of Residues	3
Details	binding site for residue SO4 B 403

Chain	Residue
B	ARG307
B	HOH506
B	HOH627

site_id	AD6
Number of Residues	5
Details	binding site for residue CA B 404

Chain	Residue
B	ASP175
B	ASP177
B	HIS179
B	SER198
B	PHE199

site_id	AD7
Number of Residues	6
Details	binding site for residue CA B 405

Chain	Residue
B	PHE188
B	THR191
B	VAL194
B	TYR223
B	HOH650
B	HOH745

site_id	AD8
Number of Residues	4
Details	binding site for residue PEG B 406

Chain	Residue
B	ASN350
B	THR352
B	HOH821
C	PEG408

site_id	AD9
Number of Residues	2
Details	binding site for residue PEG B 407

Chain	Residue
B	ASN22
B	TYR23

site_id	AE1
Number of Residues	21
Details	binding site for residue V1P B 408

Chain	Residue
B	PRO30
B	MET31
B	GLU99
B	ASP100
B	HIS141
B	HIS142
B	GLY150
B	PHE151
B	ASP177
B	HIS179
B	PHE206
B	ASP265
B	LEU272
B	GLY302
B	TYR304
B	ZN401
B	HOH502
B	HOH512
B	HOH525
B	HOH644
B	GLY28

site_id	AE2
Number of Residues	4
Details	binding site for residue ZN C 401

Chain	Residue
C	ASP177
C	HIS179
C	ASP265
C	V1P410

site_id	AE3
Number of Residues	4
Details	binding site for residue SO4 C 402

Chain	Residue
A	ARG81
C	ARG230
C	LYS362
C	HOH587

site_id	AE4
Number of Residues	7
Details	binding site for residue SO4 C 403

Chain	Residue
C	ARG271
C	TYR304
C	THR305
C	ILE306
C	ARG307
C	TYR337
C	HOH514

site_id	AE5
Number of Residues	8
Details	binding site for residue SO4 C 404

Chain	Residue
B	SER347
B	PRO348
C	LYS67
C	LYS166
C	HOH505
C	HOH507
C	HOH680
C	HOH753

site_id	AE6
Number of Residues	4
Details	binding site for residue SO4 C 405

Chain	Residue
C	HIS58
C	LYS59
C	HOH501
C	HOH569

site_id	AE7
Number of Residues	6
Details	binding site for residue CA C 406

Chain	Residue
C	PHE188
C	THR191
C	VAL194
C	TYR223
C	HOH604
C	HOH706

site_id	AE8
Number of Residues	5
Details	binding site for residue CA C 407

Chain	Residue
C	ASP175
C	ASP177
C	HIS179
C	SER198
C	PHE199

site_id	AE9
Number of Residues	7
Details	binding site for residue PEG C 408

Chain	Residue
B	ASN350
B	PEG406
C	LEU165
C	LYS166
C	TYR167
C	GLN169
C	ARG193

site_id	AF1
Number of Residues	7
Details	binding site for residue PEG C 409

Chain	Residue
C	PHE206
C	PRO207
C	GLY208
C	V1P410
C	HOH571
C	HOH589
C	HOH761

site_id	AF2
Number of Residues	22
Details	binding site for residue V1P C 410

Chain	Residue
C	GLY28
C	PRO30
C	MET31
C	GLU99
C	ASP100
C	HIS141
C	HIS142
C	GLY150
C	PHE151
C	ASP177
C	HIS179
C	PHE206
C	ASP265
C	LEU272
C	GLY302
C	TYR304
C	ZN401
C	PEG409
C	HOH502
C	HOH523
C	HOH603
C	HOH711

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	626
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)