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6FDI

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226

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
AHOH634
AHOH707

site_idAC2
Number of Residues6
Detailsbinding site for residue MG A 502
ChainResidue
AHOH704
AHOH721
AHOH755
AASP201
AHOH634
AHOH636

site_idAC3
Number of Residues6
Detailsbinding site for residue EDO A 503
ChainResidue
ASER208
APHE340
APRO356
AHOH647
AHOH668
AHOH752

site_idAC4
Number of Residues7
Detailsbinding site for residue EDO A 504
ChainResidue
ATHR148
AHIS152
AGLU243
AHOH627
CLEU212
CTHR215
CHOH690

site_idAC5
Number of Residues3
Detailsbinding site for residue EDO A 505
ChainResidue
AGLU218
AEDO520
AHOH680

site_idAC6
Number of Residues4
Detailsbinding site for residue EDO A 506
ChainResidue
AASN100
ALYS101
ATRP102
AHOH615

site_idAC7
Number of Residues6
Detailsbinding site for residue EDO A 507
ChainResidue
AGLU243
AGLU244
AASN245
AHOH644
AHOH706
AHOH784

site_idAC8
Number of Residues4
Detailsbinding site for residue EDO A 508
ChainResidue
ATHR134
ALYS136
DASP391
DEDO505

site_idAC9
Number of Residues4
Detailsbinding site for residue EDO A 509
ChainResidue
ASER259
ALYS262
ATYR303
AHOH803

site_idAD1
Number of Residues5
Detailsbinding site for residue EDO A 510
ChainResidue
AMET286
ATHR289
ALYS291
ALEU299
AHOH632

site_idAD2
Number of Residues4
Detailsbinding site for residue EDO A 511
ChainResidue
ALYS94
AGLU95
AASP98
AHIS105

site_idAD3
Number of Residues4
Detailsbinding site for residue EDO A 512
ChainResidue
APHE107
AGLU111
AARG335
AHOH740

site_idAD4
Number of Residues5
Detailsbinding site for residue PEG A 513
ChainResidue
AHIS154
AASP156
AVAL157
APRO205
CASP151

site_idAD5
Number of Residues10
Detailsbinding site for residue D5T A 514
ChainResidue
AMET273
ALEU319
AILE336
APHE340
AMET357
AGLN369
AGLY371
APHE372
AHOH661
AHOH752

site_idAD6
Number of Residues5
Detailsbinding site for residue EDO A 515
ChainResidue
ALEU175
ATHR178
ATRP384
AHOH615
AHOH664

site_idAD7
Number of Residues6
Detailsbinding site for residue EDO A 516
ChainResidue
AASN115
AALA155
AASN161
AASN162
AILE163
AHOH621

site_idAD8
Number of Residues2
Detailsbinding site for residue EDO A 517
ChainResidue
ALYS136
AHOH606

site_idAD9
Number of Residues3
Detailsbinding site for residue EDO A 518
ChainResidue
AASP140
ATHR141
AASN245

site_idAE1
Number of Residues6
Detailsbinding site for residue EDO A 519
ChainResidue
APHE238
APHE249
AARG257
AARG261
AHOH629
AHOH658

site_idAE2
Number of Residues4
Detailsbinding site for residue EDO A 520
ChainResidue
CHOH607
AGLU218
AEDO505
CHIS152

site_idAE3
Number of Residues5
Detailsbinding site for residue EDO A 521
ChainResidue
ALYS262
AASP266
AHOH635
AHOH771
BHOH675

site_idAE4
Number of Residues6
Detailsbinding site for residue EDO A 522
ChainResidue
AASN209
ASER226
ASER227
AASP272
ASER274
AHOH692

site_idAE5
Number of Residues3
Detailsbinding site for residue EDO A 523
ChainResidue
AASP266
ALEU269
AGLN311

site_idAE6
Number of Residues7
Detailsbinding site for residue EDO A 524
ChainResidue
AASN115
AARG116
AGLU150
AASP151
ATYR153
AASN162
AEDO525

site_idAE7
Number of Residues8
Detailsbinding site for residue EDO A 525
ChainResidue
AASP151
ATYR153
AHIS154
AALA155
AEDO524
AHOH770
CASP156
CHOH678

site_idAE8
Number of Residues6
Detailsbinding site for residue ZN B 501
ChainResidue
BHIS164
BHIS200
BASP201
BASP318
BHOH621
BHOH705

site_idAE9
Number of Residues6
Detailsbinding site for residue MG B 502
ChainResidue
BASP201
BHOH621
BHOH632
BHOH660
BHOH676
BHOH738

site_idAF1
Number of Residues6
Detailsbinding site for residue EDO B 503
ChainResidue
BSER208
BPHE340
BPRO356
BCYS358
BHOH618
BHOH643

site_idAF2
Number of Residues3
Detailsbinding site for residue EDO B 504
ChainResidue
BGLN331
BASP334
BARG335

site_idAF3
Number of Residues7
Detailsbinding site for residue EDO B 505
ChainResidue
BTHR144
BGLU244
BHOH617
DTHR215
DARG350
DMET352
DHOH619

site_idAF4
Number of Residues3
Detailsbinding site for residue EDO B 506
ChainResidue
BGLU366
BTHR409
BHOH619

site_idAF5
Number of Residues4
Detailsbinding site for residue EDO B 507
ChainResidue
AASN224
BLYS262
BILE265
BASP266

site_idAF6
Number of Residues3
Detailsbinding site for residue EDO B 508
ChainResidue
BGLU349
BARG350
DMET147

site_idAF7
Number of Residues5
Detailsbinding site for residue PEG B 509
ChainResidue
BASP374
BHIS378
BPRO379
BGLU382
BHOH704

site_idAF8
Number of Residues7
Detailsbinding site for residue EPE B 510
ChainResidue
BASP140
BLYS290
BVAL292
BHOH636
BHOH749
CTHR253
CLYS254

site_idAF9
Number of Residues3
Detailsbinding site for residue EDO B 511
ChainResidue
BGLU218
BHOH631
DLYS239

site_idAG1
Number of Residues11
Detailsbinding site for residue D5T B 512
ChainResidue
BMET273
BLEU319
BASN321
BILE336
BMET357
BSER368
BGLN369
BGLY371
BPHE372
BHOH601
BHOH688

site_idAG2
Number of Residues4
Detailsbinding site for residue EDO B 513
ChainResidue
BLEU175
BTHR178
BILE395
BHOH685

site_idAG3
Number of Residues3
Detailsbinding site for residue EDO B 514
ChainResidue
BARG348
BLYS360
BHIS361

site_idAG4
Number of Residues6
Detailsbinding site for residue EDO B 515
ChainResidue
BHIS105
BVAL106
BPHE107
BARG108
BLEU328
BGLN331

site_idAG5
Number of Residues4
Detailsbinding site for residue EDO B 516
ChainResidue
BASN115
BALA155
BASN161
BASN162

site_idAG6
Number of Residues5
Detailsbinding site for residue EDO C 501
ChainResidue
AHIS152
AHOH619
CGLU218
CEDO502
CHOH734

site_idAG7
Number of Residues3
Detailsbinding site for residue EDO C 502
ChainResidue
CGLU218
CEDO501
CHOH662

site_idAG8
Number of Residues5
Detailsbinding site for residue EDO C 503
ChainResidue
BPRO179
BHOH779
CLYS255
CSER259
CHOH613

site_idAG9
Number of Residues6
Detailsbinding site for residue ZN C 504
ChainResidue
CHIS164
CHIS200
CASP201
CASP318
CHOH615
CHOH680

site_idAH1
Number of Residues6
Detailsbinding site for residue MG C 505
ChainResidue
CASP201
CHOH615
CHOH634
CHOH643
CHOH668
CHOH718

site_idAH2
Number of Residues7
Detailsbinding site for residue EDO C 506
ChainResidue
AHOH613
CASN115
CARG116
CGLU150
CTYR153
CASN162
CHOH601

site_idAH3
Number of Residues4
Detailsbinding site for residue EDO C 507
ChainResidue
CSER208
CPRO356
CHOH604
CHOH722

site_idAH4
Number of Residues4
Detailsbinding site for residue EDO C 508
ChainResidue
CARG257
CARG261
CHOH610
DPG4518

site_idAH5
Number of Residues4
Detailsbinding site for residue EDO C 509
ChainResidue
CASP140
CTHR141
CASN245
CGLN250

site_idAH6
Number of Residues5
Detailsbinding site for residue EDO C 510
ChainResidue
CLEU175
CTHR178
CTRP384
CVAL388
CASP391

site_idAH7
Number of Residues2
Detailsbinding site for residue EDO C 511
ChainResidue
CASP203
CPRO205

site_idAH8
Number of Residues8
Detailsbinding site for residue EPE C 512
ChainResidue
CHIS105
CVAL106
CPHE107
CARG108
CGLU111
CGLN327
CLEU328
CGLN331

site_idAH9
Number of Residues12
Detailsbinding site for residue D5T C 513
ChainResidue
CMET273
CLEU319
CASN321
CILE336
CMET357
CSER368
CGLN369
CPHE372
CILE376
CEDO515
CHOH608
CHOH697

site_idAI1
Number of Residues5
Detailsbinding site for residue EDO C 514
ChainResidue
CASN115
CALA155
CASN162
CARG335
CHOH605

site_idAI2
Number of Residues4
Detailsbinding site for residue EDO C 515
ChainResidue
CHIS276
CMET277
CD5T513
CHOH710

site_idAI3
Number of Residues6
Detailsbinding site for residue EDO C 516
ChainResidue
CSER227
CASP272
CSER274
CLYS275
CEDO517
CHOH699

site_idAI4
Number of Residues5
Detailsbinding site for residue EDO C 517
ChainResidue
CGLN210
CEDO516
CHOH609
CHOH624
CHOH660

site_idAI5
Number of Residues7
Detailsbinding site for residue EDO C 518
ChainResidue
CPRO325
CLEU326
CASP401
CASN402
CHOH603
CHOH646
DARG330

site_idAI6
Number of Residues6
Detailsbinding site for residue EDO D 501
ChainResidue
BARG346
DASP151
DHIS152
DEDO514
DHOH601
DHOH602

site_idAI7
Number of Residues6
Detailsbinding site for residue EDO D 502
ChainResidue
AGLN258
BASN214
DSER294
DSER295
DHOH608
DHOH707

site_idAI8
Number of Residues6
Detailsbinding site for residue ZN D 503
ChainResidue
DHIS164
DHIS200
DASP201
DASP318
DHOH625
DHOH762

site_idAI9
Number of Residues6
Detailsbinding site for residue MG D 504
ChainResidue
DASP201
DHOH625
DHOH661
DHOH677
DHOH746
DHOH776

site_idAJ1
Number of Residues7
Detailsbinding site for residue EDO D 505
ChainResidue
ATHR134
APHE135
AASN251
AGLN256
AEDO508
DPRO179
DASP391

site_idAJ2
Number of Residues3
Detailsbinding site for residue EDO D 506
ChainResidue
DSER259
DLYS262
DTYR303

site_idAJ3
Number of Residues5
Detailsbinding site for residue EDO D 507
ChainResidue
DSER208
DPRO356
DHOH607
DHOH631
DHOH802

site_idAJ4
Number of Residues5
Detailsbinding site for residue EDO D 508
ChainResidue
DPHE238
DPHE249
DARG257
DHOH609
DHOH613

site_idAJ5
Number of Residues7
Detailsbinding site for residue PEG D 509
ChainResidue
BASP156
DARG116
DGLU150
DASP151
DTYR153
DALA155
DEDO520

site_idAJ6
Number of Residues5
Detailsbinding site for residue PEG D 510
ChainResidue
DMET277
DALA281
DLYS284
DHOH606
DHOH646

site_idAJ7
Number of Residues8
Detailsbinding site for residue PEG D 511
ChainResidue
AGLN250
AHOH643
BASN216
DGLN242
DGLU243
DGLU244
DASN245
DHOH790

site_idAJ8
Number of Residues7
Detailsbinding site for residue D5T D 512
ChainResidue
DMET273
DLEU319
DILE336
DMET357
DGLN369
DPHE372
DHOH627

site_idAJ9
Number of Residues7
Detailsbinding site for residue EDO D 513
ChainResidue
ALEU188
ALYS255
AGLN256
ASER259
DGLU182
DHOH603
DHOH659

site_idAK1
Number of Residues7
Detailsbinding site for residue EDO D 514
ChainResidue
BTHR215
BARG350
DTHR148
DHIS152
DGLU243
DEDO501
DHOH623

site_idAK2
Number of Residues5
Detailsbinding site for residue EDO D 515
ChainResidue
CHOH624
DLYS262
DILE265
DASP266
DHOH644

site_idAK3
Number of Residues7
Detailsbinding site for residue EDO D 516
ChainResidue
DLEU175
DTHR178
DVAL388
DASP391
DHOH604
DHOH658
DHOH749

site_idAK4
Number of Residues4
Detailsbinding site for residue EDO D 517
ChainResidue
DASP98
DLYS101
DTRP102
DHIS105

site_idAK5
Number of Residues14
Detailsbinding site for residue PG4 D 518
ChainResidue
CTYR223
CASN231
CLEU234
CALA235
CPHE238
CARG261
CEDO508
DLEU221
DMET222
DASN224
DHOH611
DHOH652
DHOH653
DHOH731

site_idAK6
Number of Residues4
Detailsbinding site for residue EDO D 519
ChainResidue
DPHE107
DGLN331
DASP334
DARG335

site_idAK7
Number of Residues6
Detailsbinding site for residue EDO D 520
ChainResidue
DASN115
DALA155
DASN162
DILE163
DPEG509
DHOH676

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

223532

PDB entries from 2024-08-07

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