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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5F2W

Crystal structure of human KDM4A in complex with compound 16

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 401

Chain	Residue
A	HIS188
A	GLU190
A	HIS276
A	5UP403

site_id	AC2
Number of Residues	3
Details	binding site for residue ZN A 402

Chain	Residue
A	CYS234
A	HIS240
A	CYS306

site_id	AC3
Number of Residues	11
Details	binding site for residue 5UP A 403

Chain	Residue
A	HIS188
A	GLU190
A	ASN198
A	LYS206
A	TRP208
A	LYS241
A	HIS276
A	ZN401
A	HOH525
A	TYR132
A	PHE185

site_id	AC4
Number of Residues	6
Details	binding site for residue EDO A 404

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

site_id	AC5
Number of Residues	2
Details	binding site for residue EDO A 405

Chain	Residue
A	PRO247
A	LEU248

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

Chain	Residue
A	GLY138
A	THR139

site_id	AC7
Number of Residues	4
Details	binding site for residue DMS A 407

Chain	Residue
A	TYR59
A	ASP63
A	ARG98
A	PHE283

site_id	AC8
Number of Residues	5
Details	binding site for residue ZN B 401

Chain	Residue
B	HIS188
B	GLU190
B	HIS276
B	5UP403
B	HOH515

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN B 402

Chain	Residue
B	CYS234
B	HIS240
B	CYS306
B	CYS308

site_id	AD1
Number of Residues	11
Details	binding site for residue 5UP B 403

Chain	Residue
B	TYR132
B	PHE185
B	HIS188
B	GLU190
B	ASN198
B	LYS206
B	TRP208
B	LYS241
B	HIS276
B	ZN401
B	HOH515

site_id	AD2
Number of Residues	3
Details	binding site for residue EDO B 404

Chain	Residue
B	ASN9
B	SER11
B	ARG13

site_id	AD3
Number of Residues	5
Details	binding site for residue EDO B 405

Chain	Residue
B	PRO10
B	SER11
B	ALA12
B	GLU214
B	HIS215

site_id	AD4
Number of Residues	3
Details	binding site for residue EDO B 406

Chain	Residue
B	PRO256
B	PHE257
B	HOH512

site_id	AD5
Number of Residues	4
Details	binding site for residue EDO B 407

Chain	Residue
B	LEU65
B	ASN137
B	GLY138
B	THR139

site_id	AD6
Number of Residues	6
Details	binding site for residue EDO B 408

Chain	Residue
B	THR83
B	PHE227
B	SER230
B	PHE237
B	HIS240
B	THR243

site_id	AD7
Number of Residues	4
Details	binding site for residue EDO B 410

Chain	Residue
B	GLU23
B	ARG29
B	PHE353
B	HOH524

site_id	AD8
Number of Residues	6
Details	binding site for residue EDO B 411

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

site_id	AD9
Number of Residues	3
Details	binding site for residue EDO B 412

Chain	Residue
B	ASP193
B	LYS217
B	TYR299

site_id	AE1
Number of Residues	5
Details	binding site for residue EDO B 413

Chain	Residue
B	ALA236
B	PHE237
B	LEU238
B	TYR275
B	HOH513

site_id	AE2
Number of Residues	5
Details	binding site for residue ZN C 401

Chain	Residue
C	HIS188
C	GLU190
C	HIS276
C	5UP403
C	HOH526

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

Chain	Residue
C	CYS308
C	CYS234
C	HIS240
C	CYS306

site_id	AE4
Number of Residues	13
Details	binding site for residue 5UP C 403

Chain	Residue
C	TYR132
C	PHE185
C	HIS188
C	GLU190
C	ASN198
C	LYS206
C	TRP208
C	HIS276
C	ZN401
C	EDO409
C	HOH520
C	HOH526
C	HOH527

site_id	AE5
Number of Residues	3
Details	binding site for residue EDO C 405

Chain	Residue
C	LEU65
C	GLY138
C	THR139

site_id	AE6
Number of Residues	1
Details	binding site for residue EDO C 406

Chain	Residue
C	GLU23

site_id	AE7
Number of Residues	7
Details	binding site for residue EDO C 407

Chain	Residue
C	ILE150
C	GLY151
C	LEU153
C	THR155
C	ASP158
C	ASN290
C	HOH516

site_id	AE8
Number of Residues	3
Details	binding site for residue EDO C 408

Chain	Residue
C	ARG295
C	GLU298
C	ASP342

site_id	AE9
Number of Residues	6
Details	binding site for residue EDO C 409

Chain	Residue
C	GLY170
C	TYR177
C	GLU190
C	SER288
C	ASN290
C	5UP403

site_id	AF1
Number of Residues	1
Details	binding site for residue EDO C 410

Chain	Residue
C	LYS217

site_id	AF2
Number of Residues	6
Details	binding site for residue EDO C 411

Chain	Residue
C	PRO10
C	SER11
C	ALA12
C	ARG41
C	GLU214
C	HIS215

site_id	AF3
Number of Residues	4
Details	binding site for residue ZN D 401

Chain	Residue
D	HIS188
D	GLU190
D	HIS276
D	5UP403

site_id	AF4
Number of Residues	4
Details	binding site for residue ZN D 402

Chain	Residue
D	CYS234
D	HIS240
D	CYS306
D	CYS308

site_id	AF5
Number of Residues	11
Details	binding site for residue 5UP D 403

Chain	Residue
D	TYR132
D	PHE185
D	HIS188
D	GLU190
D	ASN198
D	LYS206
D	TRP208
D	HIS276
D	ZN401
D	HOH528
D	HOH541

site_id	AF6
Number of Residues	4
Details	binding site for residue EDO D 404

Chain	Residue
D	GLU235
D	ALA236
D	PHE237
D	LEU238

site_id	AF7
Number of Residues	4
Details	binding site for residue EDO D 405

Chain	Residue
D	THR83
D	SER230
D	HIS240
D	THR243

site_id	AF8
Number of Residues	3
Details	binding site for residue EDO D 406

Chain	Residue
D	TRP122
D	LEU248
D	HOH549

site_id	AF9
Number of Residues	5
Details	binding site for residue EDO D 407

Chain	Residue
D	SER11
D	ALA12
D	PRO212
D	PHE257
D	EDO409

site_id	AG1
Number of Residues	5
Details	binding site for residue EDO D 408

Chain	Residue
D	PRO10
D	SER11
D	ALA12
D	GLU214
D	HIS215

site_id	AG2
Number of Residues	4
Details	binding site for residue EDO D 409

Chain	Residue
D	PHE257
D	EDO407
D	HOH519
D	HOH529

site_id	AG3
Number of Residues	7
Details	binding site for residue EDO D 410

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

site_id	AG4
Number of Residues	3
Details	binding site for residue EDO D 411

Chain	Residue
D	GLU23
D	ARG29
D	TYR30

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

224572

PDB entries from 2024-09-04

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