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6FE7

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-356

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
AHOH629
AHOH688

site_idAC2
Number of Residues6
Detailsbinding site for residue MG A 502
ChainResidue
AHOH669
AHOH710
AHOH719
AASP201
AHOH629
AHOH634

site_idAC3
Number of Residues5
Detailsbinding site for residue EDO A 503
ChainResidue
ASER208
APHE340
APRO356
ACYS358
AHOH654

site_idAC4
Number of Residues4
Detailsbinding site for residue EDO A 504
ChainResidue
AASN100
ALYS101
ATRP102
AHOH764

site_idAC5
Number of Residues5
Detailsbinding site for residue EDO A 505
ChainResidue
AGLU244
AASN245
AHOH671
AHOH681
DARG257

site_idAC6
Number of Residues6
Detailsbinding site for residue EDO A 506
ChainResidue
ATHR134
ALYS136
AHOH736
DASP391
DEDO504
DPEG519

site_idAC7
Number of Residues3
Detailsbinding site for residue EDO A 507
ChainResidue
ASER259
ATYR303
AEDO521

site_idAC8
Number of Residues7
Detailsbinding site for residue EDO A 508
ChainResidue
AMET286
ATHR289
ALYS291
ALEU298
ALEU299
ALEU300
AHOH605

site_idAC9
Number of Residues5
Detailsbinding site for residue EDO A 509
ChainResidue
APHE107
AGLU111
AGLN331
AARG335
AHOH667

site_idAD1
Number of Residues5
Detailsbinding site for residue PEG A 510
ChainResidue
AASP266
AASN278
AGLN311
AHOH615
AHOH644

site_idAD2
Number of Residues5
Detailsbinding site for residue PEG A 511
ChainResidue
AHIS154
AASP156
APRO205
CASP151
CPG4502

site_idAD3
Number of Residues4
Detailsbinding site for residue EDO A 512
ChainResidue
APHE238
AARG257
AHOH637
AHOH717

site_idAD4
Number of Residues4
Detailsbinding site for residue EDO A 513
ChainResidue
AASN115
AALA155
AASN162
AEDO523

site_idAD5
Number of Residues5
Detailsbinding site for residue EDO A 514
ChainResidue
ALEU175
ATHR178
ATRP384
AILE395
AHOH612

site_idAD6
Number of Residues5
Detailsbinding site for residue EDO A 515
ChainResidue
AHIS152
AGLU243
AHOH603
AHOH732
CEDO512

site_idAD7
Number of Residues8
Detailsbinding site for residue PEG A 516
ChainResidue
AASN209
AASP225
ASER226
ASER227
AVAL228
AASP272
ASER274
AHOH762

site_idAD8
Number of Residues7
Detailsbinding site for residue PEG A 517
ChainResidue
ALYS262
AILE265
AASP266
AHOH638
AHOH742
BASP225
BHOH661

site_idAD9
Number of Residues6
Detailsbinding site for residue PEG A 518
ChainResidue
AGLU218
AEDO522
CHIS232
CALA235
CVAL236
CLYS239

site_idAE1
Number of Residues3
Detailsbinding site for residue PEG A 519
ChainResidue
AASP98
ATRP102
AHIS105

site_idAE2
Number of Residues11
Detailsbinding site for residue D62 A 520
ChainResidue
AMET273
ALEU319
AASN321
AILE336
APRO356
AMET357
AGLN369
AGLY371
APHE372
AILE376
AHOH713

site_idAE3
Number of Residues4
Detailsbinding site for residue EDO A 521
ChainResidue
ASER259
AEDO507
AHOH601
AHOH648

site_idAE4
Number of Residues5
Detailsbinding site for residue EDO A 522
ChainResidue
AGLU218
APEG518
CHIS152
CPG4502
CHOH606

site_idAE5
Number of Residues8
Detailsbinding site for residue EDO A 523
ChainResidue
AASN115
AARG116
AGLU150
AASP151
ATYR153
AASN162
AEDO513
AEDO525

site_idAE6
Number of Residues8
Detailsbinding site for residue EPE A 524
ChainResidue
AHIS105
AVAL106
APHE107
AARG108
AGLU111
AGLN327
ALEU328
AGLN331

site_idAE7
Number of Residues7
Detailsbinding site for residue EDO A 525
ChainResidue
AASP151
ATYR153
AHIS154
AALA155
AEDO523
CASP156
CHOH654

site_idAE8
Number of Residues6
Detailsbinding site for residue ZN B 501
ChainResidue
BHIS164
BHIS200
BASP201
BASP318
BHOH616
BHOH688

site_idAE9
Number of Residues6
Detailsbinding site for residue MG B 502
ChainResidue
BASP201
BHOH616
BHOH645
BHOH649
BHOH670
BHOH724

site_idAF1
Number of Residues6
Detailsbinding site for residue EDO B 503
ChainResidue
BSER208
BPHE340
BPRO356
BCYS358
BHOH622
BHOH656

site_idAF2
Number of Residues4
Detailsbinding site for residue EDO B 504
ChainResidue
BLYS284
BGLU288
BTHR383
BASP386

site_idAF3
Number of Residues3
Detailsbinding site for residue EDO B 505
ChainResidue
BGLU366
BTYR406
BHOH620

site_idAF4
Number of Residues3
Detailsbinding site for residue EDO B 506
ChainResidue
BLYS262
BILE265
BASP266

site_idAF5
Number of Residues2
Detailsbinding site for residue EDO B 507
ChainResidue
BGLU349
BARG350

site_idAF6
Number of Residues6
Detailsbinding site for residue PEG B 508
ChainResidue
BILE373
BASP374
BHIS378
BPRO379
BGLU382
BHOH691

site_idAF7
Number of Residues9
Detailsbinding site for residue EPE B 509
ChainResidue
BASP140
BTHR141
BASN245
BGLN250
BLYS290
BVAL292
BHOH624
CTHR253
CLYS254

site_idAF8
Number of Residues4
Detailsbinding site for residue EDO B 510
ChainResidue
BGLU218
BEDO513
BHOH651
DLYS239

site_idAF9
Number of Residues5
Detailsbinding site for residue EDO B 511
ChainResidue
BASN115
BALA155
BASN162
BILE163
BEDO517

site_idAG1
Number of Residues2
Detailsbinding site for residue EDO B 512
ChainResidue
BALA183
BPHE185

site_idAG2
Number of Residues5
Detailsbinding site for residue EDO B 513
ChainResidue
BGLU218
BEDO510
BHOH638
BHOH651
DHIS152

site_idAG3
Number of Residues5
Detailsbinding site for residue EDO B 514
ChainResidue
BSER355
BMET357
BCYS358
BASP359
BASN362

site_idAG4
Number of Residues4
Detailsbinding site for residue EDO B 515
ChainResidue
BLEU175
BTHR178
BTRP384
BILE395

site_idAG5
Number of Residues11
Detailsbinding site for residue D62 B 516
ChainResidue
BMET273
BLEU319
BASN321
BILE336
BPRO356
BMET357
BSER368
BGLN369
BPHE372
BHOH686
BHOH713

site_idAG6
Number of Residues5
Detailsbinding site for residue EDO B 517
ChainResidue
BASN115
BGLU150
BTYR153
BASN162
BEDO511

site_idAG7
Number of Residues3
Detailsbinding site for residue EDO B 518
ChainResidue
BPRO205
BARG346
DASP151

site_idAG8
Number of Residues4
Detailsbinding site for residue EDO B 519
ChainResidue
BGLN210
BSER274
BHOH615
BHOH635

site_idAG9
Number of Residues7
Detailsbinding site for residue EDO B 520
ChainResidue
BHIS389
BPRO390
CTHR134
CPHE135
CLYS136
CASN251
CGLN256

site_idAH1
Number of Residues7
Detailsbinding site for residue EPE B 521
ChainResidue
BHIS105
BVAL106
BPHE107
BARG108
BGLU111
BLEU328
BGLN331

site_idAH2
Number of Residues4
Detailsbinding site for residue EDO C 501
ChainResidue
AHIS152
AHOH651
CGLU218
CEDO503

site_idAH3
Number of Residues12
Detailsbinding site for residue PG4 C 502
ChainResidue
AHIS154
AASP203
APRO205
ASER217
AARG350
APEG511
AEDO522
CTHR148
CASP151
CHIS152
CGLU243
CHOH698

site_idAH4
Number of Residues3
Detailsbinding site for residue EDO C 503
ChainResidue
AHOH607
CGLU218
CEDO501

site_idAH5
Number of Residues5
Detailsbinding site for residue EDO C 504
ChainResidue
BPRO179
CLEU188
CLYS255
CSER259
CHOH610

site_idAH6
Number of Residues6
Detailsbinding site for residue ZN C 505
ChainResidue
CHIS164
CHIS200
CASP201
CASP318
CHOH611
CHOH655

site_idAH7
Number of Residues6
Detailsbinding site for residue MG C 506
ChainResidue
CASP201
CHOH611
CHOH627
CHOH634
CHOH667
CHOH681

site_idAH8
Number of Residues6
Detailsbinding site for residue EDO C 507
ChainResidue
CASN115
CARG116
CGLU150
CASP151
CTYR153
CASN162

site_idAH9
Number of Residues4
Detailsbinding site for residue EDO C 508
ChainResidue
CSER208
CPRO356
CCYS358
CHOH696

site_idAI1
Number of Residues4
Detailsbinding site for residue EDO C 509
ChainResidue
CPHE238
CARG257
CARG261
CHOH615

site_idAI2
Number of Residues4
Detailsbinding site for residue EDO C 510
ChainResidue
CASP140
CTHR141
CASN245
CGLN250

site_idAI3
Number of Residues5
Detailsbinding site for residue EDO C 511
ChainResidue
CLEU175
CTHR178
CTRP384
CASP391
CILE395

site_idAI4
Number of Residues3
Detailsbinding site for residue EDO C 512
ChainResidue
AEDO515
CASP203
CPRO205

site_idAI5
Number of Residues4
Detailsbinding site for residue PEG C 513
ChainResidue
CASP98
CTRP102
CHIS105
CEDO516

site_idAI6
Number of Residues9
Detailsbinding site for residue EPE C 514
ChainResidue
CHIS105
CVAL106
CPHE107
CARG108
CGLU111
CGLN327
CLEU328
CGLN331
CHOH705

site_idAI7
Number of Residues6
Detailsbinding site for residue EDO C 515
ChainResidue
CPRO325
CLEU326
CASP401
CASN402
CHOH692
DARG330

site_idAI8
Number of Residues5
Detailsbinding site for residue EDO C 516
ChainResidue
CGLY103
CHIS105
CPRO325
CGLN327
CPEG513

site_idAI9
Number of Residues2
Detailsbinding site for residue EDO C 517
ChainResidue
CGLU128
CSER177

site_idAJ1
Number of Residues2
Detailsbinding site for residue EDO C 518
ChainResidue
CMET273
CMET277

site_idAJ2
Number of Residues6
Detailsbinding site for residue PEG C 519
ChainResidue
CGLN210
CSER227
CASP272
CSER274
CHOH663
CHOH675

site_idAJ3
Number of Residues10
Detailsbinding site for residue D62 C 520
ChainResidue
CMET273
CLEU319
CASN321
CILE336
CPRO356
CMET357
CGLN369
CPHE372
CILE376
CHOH652

site_idAJ4
Number of Residues11
Detailsbinding site for residue PG4 C 521
ChainResidue
CTYR223
CASN231
CLEU234
CALA235
CPHE238
CARG261
CHOH636
DLEU221
DMET222
DASN224
DHOH608

site_idAJ5
Number of Residues5
Detailsbinding site for residue EDO C 522
ChainResidue
CASN115
CALA155
CASN162
CARG335
CHOH601

site_idAJ6
Number of Residues6
Detailsbinding site for residue EDO D 501
ChainResidue
AGLN258
BASN214
BHOH714
DSER294
DSER295
DHOH601

site_idAJ7
Number of Residues6
Detailsbinding site for residue ZN D 502
ChainResidue
DHIS164
DHIS200
DASP201
DASP318
DHOH637
DHOH705

site_idAJ8
Number of Residues6
Detailsbinding site for residue MG D 503
ChainResidue
DASP201
DHOH637
DHOH638
DHOH654
DHOH702
DHOH749

site_idAJ9
Number of Residues6
Detailsbinding site for residue EDO D 504
ChainResidue
ATHR134
AASN251
AGLN256
AEDO506
DPRO179
DASP391

site_idAK1
Number of Residues6
Detailsbinding site for residue EDO D 505
ChainResidue
DSER208
DSER355
DPRO356
DCYS358
DEDO507
DHOH658

site_idAK2
Number of Residues5
Detailsbinding site for residue EDO D 506
ChainResidue
DPHE238
DPHE249
DARG257
DHOH630
DHOH645

site_idAK3
Number of Residues7
Detailsbinding site for residue EDO D 507
ChainResidue
DHIS160
DSER208
DEDO505
DD62517
DHOH616
DHOH652
DHOH666

site_idAK4
Number of Residues3
Detailsbinding site for residue PEG D 508
ChainResidue
DASP98
DTRP102
DHIS105

site_idAK5
Number of Residues8
Detailsbinding site for residue PEG D 509
ChainResidue
BASP156
BHOH673
DARG116
DGLU150
DASP151
DTYR153
DALA155
DHOH743

site_idAK6
Number of Residues5
Detailsbinding site for residue PEG D 510
ChainResidue
DASP266
DLEU269
DLYS275
DASN278
DGLN311

site_idAK7
Number of Residues4
Detailsbinding site for residue EDO D 511
ChainResidue
BTHR215
DTHR148
DHIS152
DGLU243

site_idAK8
Number of Residues3
Detailsbinding site for residue EDO D 512
ChainResidue
CHOH658
DLYS262
DASP266

site_idAK9
Number of Residues5
Detailsbinding site for residue EDO D 513
ChainResidue
DASN115
DALA155
DASN162
DILE163
DEDO520

site_idAL1
Number of Residues7
Detailsbinding site for residue EDO D 514
ChainResidue
DLEU176
DLEU181
DALA183
DVAL184
DPHE185
DILE190
DHOH679

site_idAL2
Number of Residues3
Detailsbinding site for residue EDO D 515
ChainResidue
DTHR134
DLYS136
DGLN256

site_idAL3
Number of Residues6
Detailsbinding site for residue EDO D 516
ChainResidue
ALEU188
ALYS255
AGLN256
ASER259
DGLU182
DHOH604

site_idAL4
Number of Residues11
Detailsbinding site for residue D62 D 517
ChainResidue
DMET273
DLEU319
DASN321
DILE336
DPRO356
DMET357
DSER368
DGLN369
DPHE372
DEDO507
DHOH701

site_idAL5
Number of Residues2
Detailsbinding site for residue PEG D 518
ChainResidue
BHOH702
DHIS123

site_idAL6
Number of Residues9
Detailsbinding site for residue PEG D 519
ChainResidue
AEDO506
DVAL174
DLEU175
DSER177
DTHR178
DTRP384
DVAL388
DILE395
DEDO522

site_idAL7
Number of Residues3
Detailsbinding site for residue EDO D 520
ChainResidue
DGLU111
DASN115
DEDO513

site_idAL8
Number of Residues5
Detailsbinding site for residue EDO D 521
ChainResidue
DARG129
DLEU131
DASP187
DILE190
DHOH636

site_idAL9
Number of Residues4
Detailsbinding site for residue EDO D 522
ChainResidue
DTRP102
DPEG519
DHOH620
DHOH700

site_idAM1
Number of Residues7
Detailsbinding site for residue EPE D 523
ChainResidue
DHIS105
DVAL106
DPHE107
DARG108
DGLU111
DLEU328
DGLN331

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

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PDB entries from 2024-07-17

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