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5F37

Crystal structure of human KDM4A in complex with compound 58

Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue ZN A 401
ChainResidue
AHIS188
AGLU190
AHIS276
AN5J403
AHOH504
AHOH524

site_idAC2
Number of Residues4
Detailsbinding site for residue ZN A 402
ChainResidue
ACYS308
ACYS234
AHIS240
ACYS306

site_idAC3
Number of Residues11
Detailsbinding site for residue N5J A 403
ChainResidue
ATYR132
ATYR177
APHE185
AHIS188
AASN198
ALYS206
ATRP208
ALYS241
AHIS276
AZN401
AHOH504

site_idAC4
Number of Residues6
Detailsbinding site for residue EDO A 404
ChainResidue
AGLY170
AGLU190
ASER288
ATHR289
AASN290
AHOH524

site_idAC5
Number of Residues5
Detailsbinding site for residue EDO A 405
ChainResidue
ATHR83
ASER230
AHIS240
AMET242
ATHR243

site_idAC6
Number of Residues3
Detailsbinding site for residue EDO A 406
ChainResidue
ALEU65
AGLY138
ATHR139

site_idAC7
Number of Residues5
Detailsbinding site for residue EDO A 407
ChainResidue
AILE150
AGLY151
ALEU153
AASN290
AHOH506

site_idAC8
Number of Residues4
Detailsbinding site for residue EDO A 408
ChainResidue
AASN9
APRO10
ASER11
AALA12

site_idAC9
Number of Residues7
Detailsbinding site for residue EDO A 409
ChainResidue
ASER11
AALA12
AARG13
APRO212
APHE257
AASP258
AHOH546

site_idAD1
Number of Residues4
Detailsbinding site for residue EDO A 410
ChainResidue
AALA134
AASP135
ALYS241
AHOH503

site_idAD2
Number of Residues5
Detailsbinding site for residue EDO A 411
ChainResidue
APRO50
ALYS51
ATRP53
ATYR199
AEDO415

site_idAD3
Number of Residues4
Detailsbinding site for residue EDO A 412
ChainResidue
AGLU235
AALA236
APHE237
ALEU238

site_idAD4
Number of Residues5
Detailsbinding site for residue EDO A 413
ChainResidue
ALYS251
AGLY254
AILE255
APHE257
AEDO414

site_idAD5
Number of Residues2
Detailsbinding site for residue EDO A 414
ChainResidue
APHE257
AEDO413

site_idAD6
Number of Residues2
Detailsbinding site for residue EDO A 415
ChainResidue
AHIS201
AEDO411

site_idAD7
Number of Residues3
Detailsbinding site for residue DMS A 416
ChainResidue
ATYR59
AARG98
APHE202

site_idAD8
Number of Residues6
Detailsbinding site for residue DMS A 417
ChainResidue
ALYS54
APRO55
AARG56
AALA57
AGLU142
AHIS144

site_idAD9
Number of Residues6
Detailsbinding site for residue ZN B 401
ChainResidue
BHIS188
BGLU190
BHIS276
BN5J403
BHOH540
BHOH545

site_idAE1
Number of Residues4
Detailsbinding site for residue ZN B 402
ChainResidue
BCYS234
BHIS240
BCYS306
BCYS308

site_idAE2
Number of Residues11
Detailsbinding site for residue N5J B 403
ChainResidue
BLYS241
BHIS276
BZN401
BHOH545
BTYR132
BTYR177
BPHE185
BHIS188
BASN198
BLYS206
BTRP208

site_idAE3
Number of Residues5
Detailsbinding site for residue EDO B 404
ChainResidue
BGLY170
BGLU190
BSER288
BTHR289
BHOH540

site_idAE4
Number of Residues3
Detailsbinding site for residue EDO B 405
ChainResidue
BASN9
BPRO10
BSER11

site_idAE5
Number of Residues4
Detailsbinding site for residue EDO B 406
ChainResidue
BPRO10
BALA12
BGLU214
BHIS215

site_idAE6
Number of Residues7
Detailsbinding site for residue EDO B 407
ChainResidue
BSER11
BALA12
BARG13
BPRO212
BPHE257
BASP258
BHOH578

site_idAE7
Number of Residues3
Detailsbinding site for residue EDO B 408
ChainResidue
BPRO256
BPHE257
BEDO417

site_idAE8
Number of Residues3
Detailsbinding site for residue EDO B 409
ChainResidue
BLEU65
BGLY138
BTHR139

site_idAE9
Number of Residues5
Detailsbinding site for residue EDO B 410
ChainResidue
BTHR83
BPHE227
BSER230
BHIS240
BTHR243

site_idAF1
Number of Residues6
Detailsbinding site for residue EDO B 411
ChainResidue
BILE150
BGLY151
BARG152
BLEU153
BASN290
BHOH520

site_idAF2
Number of Residues3
Detailsbinding site for residue EDO B 412
ChainResidue
BLEU8
BASN9
BGLN37

site_idAF3
Number of Residues3
Detailsbinding site for residue EDO B 413
ChainResidue
BGLU23
BARG29
BHOH583

site_idAF4
Number of Residues7
Detailsbinding site for residue EDO B 414
ChainResidue
BASN86
BALA134
BASP135
BSER184
BLYS241
BHOH507
BHOH628

site_idAF5
Number of Residues5
Detailsbinding site for residue EDO B 415
ChainResidue
BHIS188
BTHR189
BASP191
BARG239
BHOH598

site_idAF6
Number of Residues6
Detailsbinding site for residue EDO B 416
ChainResidue
BLYS224
BGLU235
BALA236
BPHE237
BLEU238
BHOH591

site_idAF7
Number of Residues5
Detailsbinding site for residue EDO B 417
ChainResidue
BLYS251
BGLY254
BILE255
BPRO256
BEDO408

site_idAF8
Number of Residues1
Detailsbinding site for residue DMS B 418
ChainResidue
BGLN88

site_idAF9
Number of Residues6
Detailsbinding site for residue ZN C 401
ChainResidue
CHIS188
CGLU190
CHIS276
CN5J403
CHOH536
CHOH561

site_idAG1
Number of Residues4
Detailsbinding site for residue ZN C 402
ChainResidue
CCYS234
CHIS240
CCYS306
CCYS308

site_idAG2
Number of Residues11
Detailsbinding site for residue N5J C 403
ChainResidue
CTYR132
CTYR177
CPHE185
CHIS188
CLYS206
CLYS241
CHIS276
CZN401
CEDO410
CHOH536
CHOH561

site_idAG3
Number of Residues6
Detailsbinding site for residue EDO C 404
ChainResidue
CGLY170
CTYR177
CGLU190
CSER288
CTHR289
CHOH536

site_idAG4
Number of Residues3
Detailsbinding site for residue EDO C 405
ChainResidue
CTHR83
CPHE227
CTHR243

site_idAG5
Number of Residues2
Detailsbinding site for residue EDO C 406
ChainResidue
CGLY138
CTHR139

site_idAG6
Number of Residues8
Detailsbinding site for residue EDO C 407
ChainResidue
CSER11
CALA12
CARG13
CPRO212
CPHE257
CASP258
CHOH531
CHOH556

site_idAG7
Number of Residues3
Detailsbinding site for residue EDO C 408
ChainResidue
CGLU23
CTYR30
CHOH527

site_idAG8
Number of Residues6
Detailsbinding site for residue EDO C 409
ChainResidue
CILE150
CGLY151
CARG152
CLEU153
CASN290
CHOH511

site_idAG9
Number of Residues5
Detailsbinding site for residue EDO C 410
ChainResidue
CALA134
CASP135
CLYS241
CN5J403
CHOH515

site_idAH1
Number of Residues3
Detailsbinding site for residue DMS C 411
ChainResidue
CTYR59
CILE62
CARG98

site_idAH2
Number of Residues6
Detailsbinding site for residue ZN D 401
ChainResidue
DHIS188
DGLU190
DHIS276
DN5J403
DHOH528
DHOH530

site_idAH3
Number of Residues4
Detailsbinding site for residue ZN D 402
ChainResidue
DCYS234
DHIS240
DCYS306
DCYS308

site_idAH4
Number of Residues12
Detailsbinding site for residue N5J D 403
ChainResidue
DTYR132
DTYR177
DPHE185
DHIS188
DASN198
DLYS206
DTRP208
DLYS241
DHIS276
DZN401
DHOH528
DHOH530

site_idAH5
Number of Residues7
Detailsbinding site for residue EDO D 404
ChainResidue
DLYS224
DGLU235
DALA236
DPHE237
DLEU238
DHOH519
DHOH601

site_idAH6
Number of Residues1
Detailsbinding site for residue EDO D 405
ChainResidue
DHIS201

site_idAH7
Number of Residues6
Detailsbinding site for residue EDO D 406
ChainResidue
DTHR83
DPHE227
DSER230
DPHE237
DTHR243
DHOH598

site_idAH8
Number of Residues7
Detailsbinding site for residue EDO D 407
ChainResidue
DSER11
DALA12
DARG13
DPRO212
DPHE257
DASP258
DHOH564

site_idAH9
Number of Residues4
Detailsbinding site for residue EDO D 408
ChainResidue
DSER11
DGLU214
DHIS215
DHOH623

site_idAI1
Number of Residues4
Detailsbinding site for residue EDO D 409
ChainResidue
DLYS251
DGLY254
DILE255
DEDO411

site_idAI2
Number of Residues4
Detailsbinding site for residue EDO D 410
ChainResidue
AGLU161
ALYS162
DARG56
DASP61

site_idAI3
Number of Residues2
Detailsbinding site for residue EDO D 411
ChainResidue
DPHE257
DEDO409

site_idAI4
Number of Residues4
Detailsbinding site for residue EDO D 412
ChainResidue
DGLU23
DARG29
DPHE353
DHOH520

site_idAI5
Number of Residues6
Detailsbinding site for residue EDO D 413
ChainResidue
DALA134
DASP135
DSER184
DLYS241
DHOH545
DHOH560

site_idAI6
Number of Residues2
Detailsbinding site for residue DMS D 414
ChainResidue
DTYR59
DARG98

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:16677698
ChainResidueDetails
ATYR132
DTYR132
DASN198
DLYS206
AASN198
ALYS206
BTYR132
BASN198
BLYS206
CTYR132
CASN198
CLYS206

site_idSWS_FT_FI2
Number of Residues8
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00538, ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168
ChainResidueDetails
AHIS188
AHIS276
BHIS188
BHIS276
CHIS188
CHIS276
DHIS188
DHIS276

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168
ChainResidueDetails
AGLU190
BGLU190
CGLU190
DGLU190

site_idSWS_FT_FI4
Number of Residues16
DetailsBINDING: 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
ChainResidueDetails
ACYS234
CHIS240
CCYS306
CCYS308
DCYS234
DHIS240
DCYS306
DCYS308
AHIS240
ACYS306
ACYS308
BCYS234
BHIS240
BCYS306
BCYS308
CCYS234

site_idSWS_FT_FI5
Number of Residues4
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:B2RXH2
ChainResidueDetails
ALYS241
BLYS241
CLYS241
DLYS241

site_idSWS_FT_FI6
Number of Residues4
DetailsMOD_RES: N-acetylalanine => ECO:0007744|PubMed:19413330
ChainResidueDetails
AALA2
BALA2
CALA2
DALA2

Catalytic Information from CSA
site_idMCSA1
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
AGLY170hydrogen bond acceptor, steric role
ATYR177hydrogen bond donor, steric role
AHIS188metal ligand
AGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
AHIS276metal ligand
ASER288hydrogen bond donor, steric role

site_idMCSA2
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
BGLY170hydrogen bond acceptor, steric role
BTYR177hydrogen bond donor, steric role
BHIS188metal ligand
BGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
BHIS276metal ligand
BSER288hydrogen bond donor, steric role

site_idMCSA3
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
CGLY170hydrogen bond acceptor, steric role
CTYR177hydrogen bond donor, steric role
CHIS188metal ligand
CGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
CHIS276metal ligand
CSER288hydrogen bond donor, steric role

site_idMCSA4
Number of Residues6
DetailsM-CSA 370
ChainResidueDetails
DGLY170hydrogen bond acceptor, steric role
DTYR177hydrogen bond donor, steric role
DHIS188metal ligand
DGLU190attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role
DHIS276metal ligand
DSER288hydrogen bond donor, steric role

222926

PDB entries from 2024-07-24

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