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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5F2S

Crystal structure of human KDM4A in complex with compound 15

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 401

Chain	Residue
A	HIS188
A	GLU190
A	HIS276
A	5TZ403
A	HOH526

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 402

Chain	Residue
A	CYS234
A	HIS240
A	CYS306
A	CYS308

site_id	AC3
Number of Residues	14
Details	binding site for residue 5TZ A 403

Chain	Residue
A	TYR132
A	TYR177
A	PHE185
A	HIS188
A	GLU190
A	LYS206
A	TRP208
A	LYS241
A	HIS276
A	ZN401
A	HOH502
A	HOH526
A	HOH533
A	HOH614

site_id	AC4
Number of Residues	7
Details	binding site for residue EDO A 404

Chain	Residue
A	GLY170
A	TYR177
A	GLU190
A	SER196
A	SER288
A	THR289
A	ASN290

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

Chain	Residue
A	THR83
A	PHE227
A	SER230
A	THR243

site_id	AC6
Number of Residues	2
Details	binding site for residue EDO A 406

Chain	Residue
A	PRO247
A	LEU248

site_id	AC7
Number of Residues	3
Details	binding site for residue EDO A 407

Chain	Residue
A	LEU65
A	GLY138
A	THR139

site_id	AC8
Number of Residues	6
Details	binding site for residue EDO A 408

Chain	Residue
A	ILE150
A	GLY151
A	ARG152
A	LEU153
A	ASN290
A	HOH534

site_id	AC9
Number of Residues	5
Details	binding site for residue EDO A 409

Chain	Residue
A	ASN9
A	PRO10
A	SER11
A	ALA12
A	ARG13

site_id	AD1
Number of Residues	5
Details	binding site for residue EDO A 410

Chain	Residue
A	SER11
A	ALA12
A	ARG13
A	PHE257
A	ASP258

site_id	AD2
Number of Residues	4
Details	binding site for residue DMS A 411

Chain	Residue
A	TYR59
A	ARG98
A	PHE202
A	PHE283

site_id	AD3
Number of Residues	2
Details	binding site for residue DMS A 412

Chain	Residue
A	LYS217
A	TYR273

site_id	AD4
Number of Residues	5
Details	binding site for residue ZN B 401

Chain	Residue
B	HIS188
B	GLU190
B	HIS276
B	5TZ403
B	HOH574

site_id	AD5
Number of Residues	4
Details	binding site for residue ZN B 402

Chain	Residue
B	CYS234
B	HIS240
B	CYS306
B	CYS308

site_id	AD6
Number of Residues	14
Details	binding site for residue 5TZ B 403

Chain	Residue
B	TYR132
B	TYR177
B	PHE185
B	HIS188
B	GLU190
B	LYS206
B	TRP208
B	HIS276
B	ZN401
B	HOH501
B	HOH550
B	HOH561
B	HOH574
B	HOH666

site_id	AD7
Number of Residues	5
Details	binding site for residue EDO B 404

Chain	Residue
B	GLY170
B	TYR177
B	GLU190
B	SER288
B	ASN290

site_id	AD8
Number of Residues	4
Details	binding site for residue EDO B 405

Chain	Residue
B	ASN9
B	PRO10
B	SER11
B	HOH603

site_id	AD9
Number of Residues	5
Details	binding site for residue EDO B 406

Chain	Residue
B	PRO10
B	ALA12
B	GLU214
B	HIS215
B	HOH559

site_id	AE1
Number of Residues	7
Details	binding site for residue EDO B 407

Chain	Residue
B	ALA12
B	ARG13
B	PRO212
B	PHE257
B	ASP258
B	HOH539
B	SER11

site_id	AE2
Number of Residues	3
Details	binding site for residue EDO B 408

Chain	Residue
B	PRO256
B	PHE257
B	HOH527

site_id	AE3
Number of Residues	3
Details	binding site for residue EDO B 409

Chain	Residue
B	LEU65
B	GLY138
B	THR139

site_id	AE4
Number of Residues	4
Details	binding site for residue EDO B 410

Chain	Residue
B	THR83
B	PHE227
B	SER230
B	THR243

site_id	AE5
Number of Residues	2
Details	binding site for residue EDO B 411

Chain	Residue
B	TRP122
B	LEU248

site_id	AE6
Number of Residues	6
Details	binding site for residue EDO B 412

Chain	Residue
B	ILE150
B	GLY151
B	ARG152
B	LEU153
B	ASN290
B	HOH507

site_id	AE7
Number of Residues	3
Details	binding site for residue EDO B 413

Chain	Residue
B	ASN9
B	GLN37
B	HOH512

site_id	AE8
Number of Residues	5
Details	binding site for residue EDO B 414

Chain	Residue
B	GLU23
B	ARG29
B	TYR33
B	PHE353
B	HOH635

site_id	AE9
Number of Residues	5
Details	binding site for residue ZN C 401

Chain	Residue
C	HIS188
C	GLU190
C	HIS276
C	5TZ403
C	HOH583

site_id	AF1
Number of Residues	4
Details	binding site for residue ZN C 402

Chain	Residue
C	CYS234
C	HIS240
C	CYS306
C	CYS308

site_id	AF2
Number of Residues	15
Details	binding site for residue 5TZ C 403

Chain	Residue
C	TYR132
C	TYR177
C	PHE185
C	HIS188
C	GLU190
C	LYS206
C	TRP208
C	LYS241
C	HIS276
C	ZN401
C	EDO404
C	HOH503
C	HOH571
C	HOH581
C	HOH583

site_id	AF3
Number of Residues	7
Details	binding site for residue EDO C 404

Chain	Residue
C	GLY170
C	TYR177
C	GLU190
C	SER288
C	THR289
C	ASN290
C	5TZ403

site_id	AF4
Number of Residues	4
Details	binding site for residue EDO C 405

Chain	Residue
C	THR83
C	PHE227
C	THR243
C	HOH616

site_id	AF5
Number of Residues	2
Details	binding site for residue EDO C 406

Chain	Residue
C	HOH552
C	HOH559

site_id	AF6
Number of Residues	3
Details	binding site for residue EDO C 407

Chain	Residue
C	LEU65
C	GLY138
C	THR139

site_id	AF7
Number of Residues	7
Details	binding site for residue EDO C 408

Chain	Residue
C	SER11
C	ALA12
C	ARG13
C	PRO212
C	PHE257
C	ASP258
C	HOH539

site_id	AF8
Number of Residues	4
Details	binding site for residue EDO C 409

Chain	Residue
C	GLU23
C	TYR30
C	TYR33
C	HOH531

site_id	AF9
Number of Residues	4
Details	binding site for residue EDO C 410

Chain	Residue
C	LYS105
C	TYR106
C	CYS107
C	HOH592

site_id	AG1
Number of Residues	6
Details	binding site for residue EDO C 411

Chain	Residue
C	ILE150
C	ARG152
C	LEU153
C	ASP158
C	ASN290
C	HOH525

site_id	AG2
Number of Residues	5
Details	binding site for residue EDO C 412

Chain	Residue
C	GLU298
C	THR339
C	VAL340
C	ASP342
C	HOH585

site_id	AG3
Number of Residues	2
Details	binding site for residue DMS C 413

Chain	Residue
C	TYR59
C	ARG98

site_id	AG4
Number of Residues	5
Details	binding site for residue ZN D 401

Chain	Residue
D	HIS188
D	GLU190
D	HIS276
D	5TZ403
D	HOH629

site_id	AG5
Number of Residues	4
Details	binding site for residue ZN D 402

Chain	Residue
D	CYS234
D	HIS240
D	CYS306
D	CYS308

site_id	AG6
Number of Residues	12
Details	binding site for residue 5TZ D 403

Chain	Residue
D	TYR132
D	TYR177
D	PHE185
D	HIS188
D	GLU190
D	LYS206
D	TRP208
D	HIS276
D	ZN401
D	HOH628
D	HOH629
D	HOH660

site_id	AG7
Number of Residues	6
Details	binding site for residue EDO D 405

Chain	Residue
D	GLY170
D	TYR177
D	GLU190
D	SER288
D	THR289
D	ASN290

site_id	AG8
Number of Residues	8
Details	binding site for residue EDO D 406

Chain	Residue
D	GLU220
D	LYS224
D	ALA236
D	PHE237
D	LEU238
D	TYR275
D	HOH520
D	HOH590

site_id	AG9
Number of Residues	2
Details	binding site for residue EDO D 407

Chain	Residue
D	HIS201
D	PHE202

site_id	AH1
Number of Residues	4
Details	binding site for residue EDO D 408

Chain	Residue
D	THR83
D	SER230
D	PHE237
D	THR243

site_id	AH2
Number of Residues	4
Details	binding site for residue EDO D 409

Chain	Residue
D	GLU118
D	TRP122
D	LEU248
D	HOH563

site_id	AH3
Number of Residues	7
Details	binding site for residue EDO D 410

Chain	Residue
D	SER11
D	ALA12
D	ARG13
D	PRO212
D	PHE257
D	ASP258
D	HOH517

site_id	AH4
Number of Residues	4
Details	binding site for residue EDO D 411

Chain	Residue
D	SER11
D	ALA12
D	GLU214
D	HIS215

site_id	AH5
Number of Residues	5
Details	binding site for residue EDO D 412

Chain	Residue
D	LYS251
D	GLY254
D	ILE255
D	PHE257
D	EDO414

site_id	AH6
Number of Residues	5
Details	binding site for residue EDO D 413

Chain	Residue
A	GLU161
A	LYS162
D	ARG56
D	ASP61
D	LEU65

site_id	AH7
Number of Residues	3
Details	binding site for residue EDO D 414

Chain	Residue
D	PRO256
D	PHE257
D	EDO412

site_id	AH8
Number of Residues	2
Details	binding site for residue DMS D 415

Chain	Residue
D	TYR59
D	ARG98

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:16677698

Chain	Residue	Details
A	TYR132
D	TYR132
D	ASN198
D	LYS206
A	ASN198
A	LYS206
B	TYR132
B	ASN198
B	LYS206
C	TYR132
C	ASN198
C	LYS206

site_id	SWS_FT_FI2
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00538, ECO:0000269\|PubMed:16677698, ECO:0000305\|PubMed:26741168

Chain	Residue	Details
A	HIS188
A	HIS276
B	HIS188
B	HIS276
C	HIS188
C	HIS276
D	HIS188
D	HIS276

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:16677698, ECO:0000305\|PubMed:26741168

Chain	Residue	Details
A	GLU190
B	GLU190
C	GLU190
D	GLU190

site_id	SWS_FT_FI4
Number of Residues	16
Details	BINDING: BINDING => ECO:0007744\|PDB:5F2W, ECO:0007744\|PDB:5F32, ECO:0007744\|PDB:5F37, ECO:0007744\|PDB:5F39, ECO:0007744\|PDB:5F3E, ECO:0007744\|PDB:5F3G, ECO:0007744\|PDB:5F5I

Chain	Residue	Details
A	CYS234
C	HIS240
C	CYS306
C	CYS308
D	CYS234
D	HIS240
D	CYS306
D	CYS308
A	HIS240
A	CYS306
A	CYS308
B	CYS234
B	HIS240
B	CYS306
B	CYS308
C	CYS234

site_id	SWS_FT_FI5
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:B2RXH2

Chain	Residue	Details
A	LYS241
B	LYS241
C	LYS241
D	LYS241

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N-acetylalanine => ECO:0007744\|PubMed:19413330

Chain	Residue	Details
A	ALA2
B	ALA2
C	ALA2
D	ALA2

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
A	GLY170	hydrogen bond acceptor, steric role
A	TYR177	hydrogen bond donor, steric role
A	HIS188	metal ligand
A	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
A	HIS276	metal ligand
A	SER288	hydrogen bond donor, steric role

site_id	MCSA2
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
B	GLY170	hydrogen bond acceptor, steric role
B	TYR177	hydrogen bond donor, steric role
B	HIS188	metal ligand
B	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
B	HIS276	metal ligand
B	SER288	hydrogen bond donor, steric role

site_id	MCSA3
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
C	GLY170	hydrogen bond acceptor, steric role
C	TYR177	hydrogen bond donor, steric role
C	HIS188	metal ligand
C	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
C	HIS276	metal ligand
C	SER288	hydrogen bond donor, steric role

site_id	MCSA4
Number of Residues	6
Details	M-CSA 370

Chain	Residue	Details
D	GLY170	hydrogen bond acceptor, steric role
D	TYR177	hydrogen bond donor, steric role
D	HIS188	metal ligand
D	GLU190	attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
D	HIS276	metal ligand
D	SER288	hydrogen bond donor, steric role

237423

PDB entries from 2025-06-11

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