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6FET

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439

Functional Information from GO Data
ChainGOidnamespacecontents
A0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
A0007165biological_processsignal transduction
A0008081molecular_functionphosphoric diester hydrolase activity
B0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
B0007165biological_processsignal transduction
B0008081molecular_functionphosphoric diester hydrolase activity
C0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
C0007165biological_processsignal transduction
C0008081molecular_functionphosphoric diester hydrolase activity
D0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
D0007165biological_processsignal transduction
D0008081molecular_functionphosphoric diester hydrolase activity
Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue ZN A 501
ChainResidue
AHIS164
AHIS200
AASP201
AASP318
AHOH618
AHOH674

site_idAC2
Number of Residues6
Detailsbinding site for residue MG A 502
ChainResidue
AHOH644
AHOH704
AHOH725
AASP201
AHOH618
AHOH624

site_idAC3
Number of Residues6
Detailsbinding site for residue EDO A 503
ChainResidue
ASER208
APHE340
APRO356
ACYS358
AHOH634
AHOH726

site_idAC4
Number of Residues5
Detailsbinding site for residue EDO A 504
ChainResidue
AHIS152
AGLU243
AHOH740
CSER217
CARG350

site_idAC5
Number of Residues2
Detailsbinding site for residue EDO A 505
ChainResidue
AGLU218
AHOH630

site_idAC6
Number of Residues4
Detailsbinding site for residue EDO A 506
ChainResidue
AGLN210
AILE213
AHOH615
AHOH690

site_idAC7
Number of Residues4
Detailsbinding site for residue EDO A 507
ChainResidue
AGLU244
AASN245
AHOH633
DARG257

site_idAC8
Number of Residues5
Detailsbinding site for residue EDO A 508
ChainResidue
ATHR134
ALYS136
DASP391
DEDO506
DPEG519

site_idAC9
Number of Residues4
Detailsbinding site for residue EDO A 509
ChainResidue
ASER259
ATYR303
AEDO521
AHOH758

site_idAD1
Number of Residues6
Detailsbinding site for residue PEG A 510
ChainResidue
AASP266
ALEU269
ALYS275
AASN278
AASP282
AGLN311

site_idAD2
Number of Residues5
Detailsbinding site for residue EDO A 511
ChainResidue
ALEU175
ATHR178
ATRP384
AASP391
AILE395

site_idAD3
Number of Residues4
Detailsbinding site for residue EDO A 512
ChainResidue
AASN115
AALA155
AASN161
AASN162

site_idAD4
Number of Residues5
Detailsbinding site for residue EDO A 513
ChainResidue
ALYS262
AILE265
AASP266
BHOH647
BHOH664

site_idAD5
Number of Residues5
Detailsbinding site for residue EDO A 514
ChainResidue
APHE238
APHE249
AARG257
AHOH621
AHOH648

site_idAD6
Number of Residues3
Detailsbinding site for residue EDO A 515
ChainResidue
ASER226
AASN231
BSER226

site_idAD7
Number of Residues5
Detailsbinding site for residue EDO A 516
ChainResidue
AASN115
AARG116
AGLU150
AASP151
ATYR153

site_idAD8
Number of Residues17
Detailsbinding site for residue D68 A 517
ChainResidue
AMET273
ALEU319
AASN321
APRO322
ATYR329
ATRP332
ATHR333
AILE336
APHE340
APRO356
AMET357
ASER368
AGLN369
AGLY371
APHE372
AILE376
AHOH710

site_idAD9
Number of Residues8
Detailsbinding site for residue EPE A 518
ChainResidue
AGLN331
AHIS105
AVAL106
APHE107
AARG108
AGLU111
AGLN327
ALEU328

site_idAE1
Number of Residues3
Detailsbinding site for residue EDO A 519
ChainResidue
ATHR119
AHIS123
AEDO520

site_idAE2
Number of Residues2
Detailsbinding site for residue EDO A 520
ChainResidue
ASER113
AEDO519

site_idAE3
Number of Residues6
Detailsbinding site for residue EDO A 521
ChainResidue
ATHR186
AGLU189
ASER259
AEDO509
AHOH628
DEDO516

site_idAE4
Number of Residues3
Detailsbinding site for residue EDO A 522
ChainResidue
AASP140
ATHR141
AASN245

site_idAE5
Number of Residues4
Detailsbinding site for residue EDO A 523
ChainResidue
AASP187
AHOH730
DLYS101
DHOH731

site_idAE6
Number of Residues6
Detailsbinding site for residue EDO A 524
ChainResidue
ALEU176
ALEU181
AALA183
AVAL184
APHE185
AILE190

site_idAE7
Number of Residues5
Detailsbinding site for residue NI A 525
ChainResidue
AHIS154
AASP156
AHOH744
CHIS154
CHOH604

site_idAE8
Number of Residues6
Detailsbinding site for residue ZN B 501
ChainResidue
BHIS164
BHIS200
BASP201
BASP318
BHOH613
BHOH698

site_idAE9
Number of Residues6
Detailsbinding site for residue MG B 502
ChainResidue
BASP201
BHOH613
BHOH631
BHOH648
BHOH652
BHOH709

site_idAF1
Number of Residues6
Detailsbinding site for residue EDO B 503
ChainResidue
BSER208
BPHE340
BPRO356
BCYS358
BHOH603
BHOH684

site_idAF2
Number of Residues4
Detailsbinding site for residue EDO B 504
ChainResidue
BPHE107
BGLN331
BASP334
BARG335

site_idAF3
Number of Residues2
Detailsbinding site for residue EDO B 505
ChainResidue
BGLU366
BTRP405

site_idAF4
Number of Residues5
Detailsbinding site for residue EDO B 506
ChainResidue
AASN224
AASP225
BLYS262
BILE265
BASP266

site_idAF5
Number of Residues11
Detailsbinding site for residue EPE B 507
ChainResidue
BASP140
BTHR141
BASN245
BGLN250
BLYS290
BVAL292
BEDO522
BHOH607
CTHR253
CLYS254
CEDO502

site_idAF6
Number of Residues4
Detailsbinding site for residue EDO B 508
ChainResidue
BPRO205
BARG346
DASP151
DEDO511

site_idAF7
Number of Residues3
Detailsbinding site for residue EDO B 509
ChainResidue
BTHR178
BASP391
BILE395

site_idAF8
Number of Residues4
Detailsbinding site for residue EDO B 510
ChainResidue
BASN115
BALA155
BASN162
BILE163

site_idAF9
Number of Residues5
Detailsbinding site for residue EDO B 511
ChainResidue
BMET286
BTHR289
BLYS291
BLEU298
BLEU299

site_idAG1
Number of Residues4
Detailsbinding site for residue PEG B 512
ChainResidue
AHOH718
BARG257
BHOH708
BHOH715

site_idAG2
Number of Residues8
Detailsbinding site for residue EPE B 513
ChainResidue
BHIS105
BVAL106
BPHE107
BARG108
BGLU111
BGLN327
BLEU328
BGLN331

site_idAG3
Number of Residues16
Detailsbinding site for residue D68 B 514
ChainResidue
BMET273
BLEU319
BASN321
BPRO322
BTYR329
BTRP332
BTHR333
BILE336
BPHE340
BMET357
BSER368
BGLN369
BGLY371
BPHE372
BILE376
BHOH674

site_idAG4
Number of Residues3
Detailsbinding site for residue EDO B 515
ChainResidue
BLYS101
BTRP102
BEDO518

site_idAG5
Number of Residues5
Detailsbinding site for residue EDO B 516
ChainResidue
BGLU150
BASP151
BTYR153
BALA155
BASN162

site_idAG6
Number of Residues2
Detailsbinding site for residue EDO B 517
ChainResidue
BLYS360
BHIS361

site_idAG7
Number of Residues3
Detailsbinding site for residue EDO B 518
ChainResidue
BASP98
BHIS105
BEDO515

site_idAG8
Number of Residues2
Detailsbinding site for residue EDO B 519
ChainResidue
BGLU111
BARG335

site_idAG9
Number of Residues2
Detailsbinding site for residue EDO B 520
ChainResidue
BASN209
BASP272

site_idAH1
Number of Residues5
Detailsbinding site for residue EDO B 521
ChainResidue
BHIS152
BGLU243
BHOH716
DTHR215
DSER217

site_idAH2
Number of Residues6
Detailsbinding site for residue EDO B 522
ChainResidue
BASN245
BLYS291
BVAL292
BLEU299
BEPE507
CEDO502

site_idAH3
Number of Residues4
Detailsbinding site for residue EDO C 501
ChainResidue
AGLU218
CHIS152
CLYS239
CHOH602

site_idAH4
Number of Residues5
Detailsbinding site for residue EDO C 502
ChainResidue
BGLU244
BVAL292
BEPE507
BEDO522
CLYS254

site_idAH5
Number of Residues5
Detailsbinding site for residue EDO C 503
ChainResidue
BPRO179
CLYS255
CSER259
CHOH616
CHOH629

site_idAH6
Number of Residues6
Detailsbinding site for residue ZN C 504
ChainResidue
CHIS164
CHIS200
CASP201
CASP318
CHOH607
CHOH676

site_idAH7
Number of Residues6
Detailsbinding site for residue MG C 505
ChainResidue
CASP201
CHOH607
CHOH627
CHOH628
CHOH668
CHOH683

site_idAH8
Number of Residues6
Detailsbinding site for residue EDO C 506
ChainResidue
CASN115
CARG116
CGLU150
CASP151
CTYR153
CASN162

site_idAH9
Number of Residues3
Detailsbinding site for residue EDO C 507
ChainResidue
CSER208
CPRO356
CCYS358

site_idAI1
Number of Residues4
Detailsbinding site for residue EDO C 508
ChainResidue
CPHE238
CARG257
CARG261
CHOH606

site_idAI2
Number of Residues4
Detailsbinding site for residue EDO C 509
ChainResidue
CPRO138
CASP140
CTHR141
CASN245

site_idAI3
Number of Residues5
Detailsbinding site for residue EDO C 510
ChainResidue
CLEU175
CTHR178
CTRP384
CALA392
CILE395

site_idAI4
Number of Residues5
Detailsbinding site for residue PEG C 511
ChainResidue
ALEU212
CASP151
CHIS152
CGLU243
CHOH678

site_idAI5
Number of Residues9
Detailsbinding site for residue EPE C 512
ChainResidue
CHIS105
CVAL106
CPHE107
CARG108
CGLU111
CGLN327
CLEU328
CGLN331
CHOH710

site_idAI6
Number of Residues6
Detailsbinding site for residue EDO C 513
ChainResidue
CPRO325
CLEU326
CASP401
CASN402
CHOH617
DARG330

site_idAI7
Number of Residues5
Detailsbinding site for residue PG4 C 514
ChainResidue
CGLU95
CASP98
CTRP102
CHIS105
CPRO325

site_idAI8
Number of Residues13
Detailsbinding site for residue D68 C 515
ChainResidue
CHIS160
CMET273
CASN321
CPRO322
CTRP332
CTHR333
CILE336
CPHE340
CMET357
CGLN369
CPHE372
CILE376
CHOH674

site_idAI9
Number of Residues6
Detailsbinding site for residue EDO C 516
ChainResidue
BHIS389
CTHR134
CPHE135
CLYS136
CASN251
CGLN256

site_idAJ1
Number of Residues6
Detailsbinding site for residue EDO C 517
ChainResidue
CASN115
CALA155
CASN161
CASN162
CARG335
CHOH660

site_idAJ2
Number of Residues3
Detailsbinding site for residue EDO C 518
ChainResidue
CLYS262
CASP266
DASN224

site_idAJ3
Number of Residues2
Detailsbinding site for residue EDO D 501
ChainResidue
BGLU349
DTHR144

site_idAJ4
Number of Residues10
Detailsbinding site for residue PG4 D 502
ChainResidue
CTYR223
CASN231
CLEU234
CALA235
CPHE238
CARG261
DLEU221
DMET222
DASN224
DHOH625

site_idAJ5
Number of Residues5
Detailsbinding site for residue EDO D 503
ChainResidue
AGLN258
BASN214
DSER294
DSER295
DHOH618

site_idAJ6
Number of Residues6
Detailsbinding site for residue ZN D 504
ChainResidue
DHIS164
DHIS200
DASP201
DASP318
DHOH617
DHOH715

site_idAJ7
Number of Residues6
Detailsbinding site for residue MG D 505
ChainResidue
DASP201
DHOH617
DHOH634
DHOH647
DHOH677
DHOH716

site_idAJ8
Number of Residues7
Detailsbinding site for residue EDO D 506
ChainResidue
ATHR134
APHE135
AASN251
AGLN256
AEDO508
DPRO179
DASP391

site_idAJ9
Number of Residues3
Detailsbinding site for residue EDO D 507
ChainResidue
DSER259
DLYS262
DTYR303

site_idAK1
Number of Residues4
Detailsbinding site for residue EDO D 508
ChainResidue
DSER208
DPRO356
DCYS358
DHOH638

site_idAK2
Number of Residues6
Detailsbinding site for residue EDO D 509
ChainResidue
DPHE238
DPHE249
DARG257
DARG261
DHOH643
DHOH691

site_idAK3
Number of Residues10
Detailsbinding site for residue EDO D 510
ChainResidue
DHIS160
DHIS204
DGLY206
DVAL207
DSER208
DGLU339
DD68520
DHOH638
DHOH655
DHOH717

site_idAK4
Number of Residues5
Detailsbinding site for residue EDO D 511
ChainResidue
BTHR215
BEDO508
DTHR148
DHIS152
DGLU243

site_idAK5
Number of Residues3
Detailsbinding site for residue EDO D 512
ChainResidue
CHOH649
DLYS262
DASP266

site_idAK6
Number of Residues4
Detailsbinding site for residue EDO D 513
ChainResidue
DASN115
DALA155
DASN162
DILE163

site_idAK7
Number of Residues4
Detailsbinding site for residue EDO D 514
ChainResidue
DARG129
DLEU131
DASP187
DILE190

site_idAK8
Number of Residues7
Detailsbinding site for residue EDO D 515
ChainResidue
DLEU176
DLEU181
DALA183
DVAL184
DPHE185
DILE190
DHOH709

site_idAK9
Number of Residues6
Detailsbinding site for residue EDO D 516
ChainResidue
ALYS255
AGLN256
ASER259
AEDO521
DGLU182
DHOH604

site_idAL1
Number of Residues4
Detailsbinding site for residue EDO D 517
ChainResidue
DTHR134
DLYS136
DASN251
DGLN256

site_idAL2
Number of Residues5
Detailsbinding site for residue EDO D 518
ChainResidue
CSER226
DSER226
DASN231
DHOH644
DHOH710

site_idAL3
Number of Residues7
Detailsbinding site for residue PEG D 519
ChainResidue
AEDO508
DVAL174
DTHR178
DTRP384
DVAL388
DASP391
DALA392

site_idAL4
Number of Residues16
Detailsbinding site for residue D68 D 520
ChainResidue
DMET273
DLEU319
DASN321
DPRO322
DTYR329
DTRP332
DTHR333
DILE336
DPHE340
DMET357
DSER368
DGLN369
DGLY371
DPHE372
DEDO510
DHOH690

site_idAL5
Number of Residues8
Detailsbinding site for residue EPE D 521
ChainResidue
DHIS105
DVAL106
DPHE107
DARG108
DGLU111
DGLN327
DLEU328
DGLN331

site_idAL6
Number of Residues1
Detailsbinding site for residue EDO D 522
ChainResidue
DGLN393

site_idAL7
Number of Residues1
Detailsbinding site for residue EDO D 523
ChainResidue
DHIS123

site_idAL8
Number of Residues4
Detailsbinding site for residue EDO D 524
ChainResidue
DMET273
DSER274
DHIS276
DMET277

site_idAL9
Number of Residues2
Detailsbinding site for residue EDO D 525
ChainResidue
DSER355
DMET357

site_idAM1
Number of Residues2
Detailsbinding site for residue EDO D 526
ChainResidue
DASP266
DGLN311

site_idAM2
Number of Residues5
Detailsbinding site for residue NI D 527
ChainResidue
BHIS154
BHOH628
DHIS154
DASP156
DHOH671

Functional Information from PROSITE/UniProt
site_idPS00126
Number of Residues12
DetailsPDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDVdHpGvsNqF
ChainResidueDetails
AHIS200-PHE211

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Proton donor => ECO:0000250|UniProtKB:Q07343
ChainResidueDetails
AHIS160
BHIS160
CHIS160
DHIS160

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7
ChainResidueDetails
AHIS160
DHIS160
DASN321
DGLN369
AASN321
AGLN369
BHIS160
BASN321
BGLN369
CHIS160
CASN321
CGLN369

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:2PW3
ChainResidueDetails
AHIS164
BHIS164
CHIS164
DHIS164

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:1XOR, ECO:0007744|PDB:2PW3
ChainResidueDetails
AHIS200
AASP318
BHIS200
BASP318
CHIS200
CASP318
DHIS200
DASP318

site_idSWS_FT_FI5
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW
ChainResidueDetails
AASP201
APHE372
BASP201
BPHE372
CASP201
CPHE372
DASP201
DPHE372

site_idSWS_FT_FI6
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)
ChainResidueDetails
ALYS85
BLYS85
CLYS85
DLYS85

218853

PDB entries from 2024-04-24

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