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6FTW

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-048

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
AHOH626
AHOH649

site_idAC2
Number of Residues6
Detailsbinding site for residue MG A 502
ChainResidue
AHOH628
AHOH688
AHOH717
AASP201
AHOH613
AHOH626

site_idAC3
Number of Residues5
Detailsbinding site for residue EDO A 503
ChainResidue
ASER208
APRO356
ACYS358
AE6Z517
AHOH618

site_idAC4
Number of Residues5
Detailsbinding site for residue EDO A 504
ChainResidue
AASN115
AALA155
AASN161
AASN162
AARG335

site_idAC5
Number of Residues5
Detailsbinding site for residue EDO A 505
ChainResidue
ATHR186
AGLU189
ASER259
AMET263
AEDO512

site_idAC6
Number of Residues6
Detailsbinding site for residue EDO A 506
ChainResidue
AGLU218
AHOH722
CHIS152
CLYS239
CLEU240
CHOH614

site_idAC7
Number of Residues4
Detailsbinding site for residue EDO A 507
ChainResidue
ALEU175
ATHR178
ATRP384
AASP391

site_idAC8
Number of Residues3
Detailsbinding site for residue EDO A 508
ChainResidue
ATHR134
ALYS136
AEDO509

site_idAC9
Number of Residues5
Detailsbinding site for residue EDO A 509
ChainResidue
ATHR134
APHE135
AASN251
AGLN256
AEDO508

site_idAD1
Number of Residues4
Detailsbinding site for residue EDO A 510
ChainResidue
AHIS152
AGLU243
CSER217
CARG350

site_idAD2
Number of Residues6
Detailsbinding site for residue EDO A 511
ChainResidue
APHE238
APHE249
AARG257
AARG261
AHOH633
AHOH642

site_idAD3
Number of Residues6
Detailsbinding site for residue EDO A 512
ChainResidue
ASER259
ALYS262
ATYR303
AEDO505
AEDO514
AHOH660

site_idAD4
Number of Residues7
Detailsbinding site for residue EDO A 513
ChainResidue
AARG116
AGLU150
AASP151
ATYR153
AHOH604
AHOH719
CEDO510

site_idAD5
Number of Residues3
Detailsbinding site for residue EDO A 514
ChainResidue
AEDO512
AHOH602
AHOH721

site_idAD6
Number of Residues9
Detailsbinding site for residue EPE A 515
ChainResidue
AHIS105
AVAL106
APHE107
AARG108
AGLU111
AGLN327
ALEU328
AGLN331
AHOH691

site_idAD7
Number of Residues5
Detailsbinding site for residue EDO A 516
ChainResidue
ALYS262
AASP266
AHOH700
BHOH619
BHOH655

site_idAD8
Number of Residues15
Detailsbinding site for residue E6Z A 517
ChainResidue
AHOH717
AMET273
AASP318
ALEU319
ATHR333
AILE336
AMET337
AMET357
ASER368
AGLN369
APHE372
AILE376
AEDO503
AHOH618
AHOH693

site_idAD9
Number of Residues6
Detailsbinding site for residue ZN B 501
ChainResidue
BHIS164
BHIS200
BASP201
BASP318
BHOH626
BHOH673

site_idAE1
Number of Residues6
Detailsbinding site for residue MG B 502
ChainResidue
BASP201
BHOH614
BHOH626
BHOH646
BHOH654
BHOH658

site_idAE2
Number of Residues3
Detailsbinding site for residue EDO B 503
ChainResidue
BSER208
BPRO356
BHOH630

site_idAE3
Number of Residues5
Detailsbinding site for residue EDO B 504
ChainResidue
BGLU218
BEDO507
BHOH632
CMET222
DLYS239

site_idAE4
Number of Residues4
Detailsbinding site for residue EDO B 505
ChainResidue
BASN115
BALA155
BASN162
BARG335

site_idAE5
Number of Residues6
Detailsbinding site for residue EDO B 506
ChainResidue
BPHE211
BASN214
BGLU347
BMET352
BGLU353
BSER355

site_idAE6
Number of Residues3
Detailsbinding site for residue EDO B 507
ChainResidue
BGLU218
BEDO504
DLYS239

site_idAE7
Number of Residues8
Detailsbinding site for residue EPE B 508
ChainResidue
BHIS105
BVAL106
BPHE107
BARG108
BGLU111
BGLN327
BLEU328
BGLN331

site_idAE8
Number of Residues11
Detailsbinding site for residue E6Z B 509
ChainResidue
BMET273
BASP318
BILE336
BMET337
BMET357
BVAL365
BSER368
BGLN369
BPHE372
BHOH671
BHOH673

site_idAE9
Number of Residues6
Detailsbinding site for residue ZN C 501
ChainResidue
CHIS164
CHIS200
CASP201
CASP318
CHOH625
CHOH658

site_idAF1
Number of Residues6
Detailsbinding site for residue MG C 502
ChainResidue
CASP201
CHOH607
CHOH625
CHOH645
CHOH657
CHOH675

site_idAF2
Number of Residues4
Detailsbinding site for residue EDO C 503
ChainResidue
CPHE249
CARG257
CHOH605
CHOH653

site_idAF3
Number of Residues4
Detailsbinding site for residue EDO C 504
ChainResidue
CLEU175
CTHR178
CTRP384
CALA392

site_idAF4
Number of Residues3
Detailsbinding site for residue EDO C 505
ChainResidue
ALYS239
BMET222
CGLU218

site_idAF5
Number of Residues3
Detailsbinding site for residue EDO C 506
ChainResidue
CTHR148
CHIS152
CGLU243

site_idAF6
Number of Residues5
Detailsbinding site for residue EDO C 507
ChainResidue
CASN115
CARG116
CGLU150
CASP151
CTYR153

site_idAF7
Number of Residues3
Detailsbinding site for residue EDO C 508
ChainResidue
CPRO356
CE6Z512
CHOH638

site_idAF8
Number of Residues3
Detailsbinding site for residue EDO C 509
ChainResidue
CLYS262
CASP266
DASP225

site_idAF9
Number of Residues5
Detailsbinding site for residue EDO C 510
ChainResidue
AGLY114
AASN115
AEDO513
CARG342
CHOH619

site_idAG1
Number of Residues8
Detailsbinding site for residue EPE C 511
ChainResidue
CHIS105
CVAL106
CPHE107
CARG108
CGLU111
CGLN327
CLEU328
CGLN331

site_idAG2
Number of Residues12
Detailsbinding site for residue E6Z C 512
ChainResidue
CHIS160
CMET273
CLEU319
CILE336
CMET337
CMET357
CSER368
CGLN369
CPHE372
CEDO508
CHOH638
CHOH656

site_idAG3
Number of Residues3
Detailsbinding site for residue EDO C 513
ChainResidue
CASN214
CGLU353
DGLN258

site_idAG4
Number of Residues6
Detailsbinding site for residue ZN D 501
ChainResidue
DHIS164
DHIS200
DASP201
DASP318
DHOH617
DHOH654

site_idAG5
Number of Residues6
Detailsbinding site for residue MG D 502
ChainResidue
DASP201
DHOH617
DHOH652
DHOH671
DHOH689
DHOH709

site_idAG6
Number of Residues4
Detailsbinding site for residue EDO D 503
ChainResidue
DSER294
DSER295
DHOH609
DHOH660

site_idAG7
Number of Residues4
Detailsbinding site for residue EDO D 504
ChainResidue
DPHE340
DPRO356
DCYS358
DE6Z516

site_idAG8
Number of Residues5
Detailsbinding site for residue EDO D 505
ChainResidue
DPHE238
DARG257
DARG261
DHOH647
DHOH672

site_idAG9
Number of Residues4
Detailsbinding site for residue EDO D 506
ChainResidue
CHOH621
DLYS262
DASP266
DHOH657

site_idAH1
Number of Residues4
Detailsbinding site for residue EDO D 507
ChainResidue
DASN115
DALA155
DASN161
DASN162

site_idAH2
Number of Residues6
Detailsbinding site for residue EDO D 508
ChainResidue
DLEU175
DTHR178
DTRP384
DVAL388
DASP391
DHOH662

site_idAH3
Number of Residues6
Detailsbinding site for residue EDO D 509
ChainResidue
DGLN250
DLEU252
DTHR253
DARG257
DHOH632
DHOH728

site_idAH4
Number of Residues4
Detailsbinding site for residue EDO D 510
ChainResidue
DARG129
DLEU131
DASP187
DILE190

site_idAH5
Number of Residues1
Detailsbinding site for residue EDO D 511
ChainResidue
DGLU182

site_idAH6
Number of Residues1
Detailsbinding site for residue EDO D 512
ChainResidue
DGLN393

site_idAH7
Number of Residues1
Detailsbinding site for residue EDO D 513
ChainResidue
DASP98

site_idAH8
Number of Residues7
Detailsbinding site for residue EPE D 514
ChainResidue
CASP394
DHIS105
DVAL106
DPHE107
DARG108
DLEU328
DGLN331

site_idAH9
Number of Residues2
Detailsbinding site for residue EDO D 515
ChainResidue
DHIS152
DGLU243

site_idAI1
Number of Residues10
Detailsbinding site for residue E6Z D 516
ChainResidue
DMET273
DASP318
DLEU319
DILE336
DMET337
DMET357
DSER368
DGLN369
DPHE372
DEDO504

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

226707

PDB entries from 2024-10-30

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