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6FW3

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-007

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
AHOH617
AHOH769

site_idAC2
Number of Residues6
Detailsbinding site for residue MG A 502
ChainResidue
AHOH685
AHOH714
AHOH779
AASP201
AHOH617
AHOH664

site_idAC3
Number of Residues4
Detailsbinding site for residue EDO A 503
ChainResidue
ASER208
APRO356
ACYS358
AHOH743

site_idAC4
Number of Residues7
Detailsbinding site for residue EDO A 504
ChainResidue
ATHR148
AHIS152
AGLU243
AHOH610
AHOH651
CLEU212
CTHR215

site_idAC5
Number of Residues4
Detailsbinding site for residue EDO A 505
ChainResidue
AGLU218
AEDO516
AHOH748
CALA235

site_idAC6
Number of Residues4
Detailsbinding site for residue EDO A 506
ChainResidue
AASN100
ALYS101
ATRP102
AHOH757

site_idAC7
Number of Residues5
Detailsbinding site for residue EDO A 507
ChainResidue
AGLU243
AGLU244
AASN245
AHOH735
AHOH798

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

site_idAC9
Number of Residues3
Detailsbinding site for residue EDO A 509
ChainResidue
ASER259
ALYS262
ATYR303

site_idAD1
Number of Residues4
Detailsbinding site for residue EDO A 510
ChainResidue
AMET286
ATHR289
ALYS291
ALEU299

site_idAD2
Number of Residues7
Detailsbinding site for residue PEG A 511
ChainResidue
AHIS154
AASP156
AVAL157
APRO205
CASP151
CHIS152
CEDO516

site_idAD3
Number of Residues5
Detailsbinding site for residue EDO A 512
ChainResidue
ATHR178
ATRP384
AVAL388
AHOH695
AHOH757

site_idAD4
Number of Residues7
Detailsbinding site for residue EDO A 513
ChainResidue
AASN115
AALA155
AASN162
AILE163
AARG335
AHOH603
AHOH699

site_idAD5
Number of Residues3
Detailsbinding site for residue EDO A 514
ChainResidue
ALYS136
AASN251
AHOH788

site_idAD6
Number of Residues6
Detailsbinding site for residue EDO A 515
ChainResidue
APHE238
AARG257
AARG261
AHOH626
AHOH752
AHOH786

site_idAD7
Number of Residues4
Detailsbinding site for residue EDO A 516
ChainResidue
AGLU218
AEDO505
CHIS152
CHOH610

site_idAD8
Number of Residues4
Detailsbinding site for residue EDO A 517
ChainResidue
ALYS262
AASP266
BHOH662
BHOH708

site_idAD9
Number of Residues7
Detailsbinding site for residue EDO A 518
ChainResidue
AASN209
ASER226
ASER227
AASP272
ASER274
AHOH652
AHOH710

site_idAE1
Number of Residues8
Detailsbinding site for residue EDO A 519
ChainResidue
AASP266
ALEU269
AALA270
ALYS275
AGLN311
AHOH650
AHOH708
AHOH756

site_idAE2
Number of Residues8
Detailsbinding site for residue EDO A 520
ChainResidue
AARG116
AGLU150
AASP151
ATYR153
AASN162
AEDO524
AHOH603
AASN115

site_idAE3
Number of Residues10
Detailsbinding site for residue EPE A 521
ChainResidue
AHIS105
AVAL106
APHE107
AARG108
APRO325
ALEU326
AGLN327
ALEU328
AGLN331
BSER408

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

site_idAE5
Number of Residues8
Detailsbinding site for residue E8H A 523
ChainResidue
AMET273
ALEU319
AASN321
AILE336
AMET357
AGLN369
APHE372
AHOH753

site_idAE6
Number of Residues7
Detailsbinding site for residue EDO A 524
ChainResidue
AASP151
ATYR153
AHIS154
AALA155
AEDO520
AHOH772
CASP156

site_idAE7
Number of Residues6
Detailsbinding site for residue EDO A 525
ChainResidue
AHIS152
AHOH638
AHOH741
CGLU218
CEDO501
CHOH738

site_idAE8
Number of Residues6
Detailsbinding site for residue ZN B 501
ChainResidue
BHIS164
BHIS200
BASP201
BASP318
BHOH610
BHOH711

site_idAE9
Number of Residues6
Detailsbinding site for residue MG B 502
ChainResidue
BASP201
BHOH610
BHOH626
BHOH634
BHOH735
BHOH745

site_idAF1
Number of Residues4
Detailsbinding site for residue EDO B 503
ChainResidue
BSER208
BPHE340
BPRO356
BCYS358

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

site_idAF3
Number of Residues2
Detailsbinding site for residue EDO B 505
ChainResidue
BGLU366
BTHR409

site_idAF4
Number of Residues3
Detailsbinding site for residue EDO B 506
ChainResidue
AASP225
BLYS262
BASP266

site_idAF5
Number of Residues8
Detailsbinding site for residue EPE B 507
ChainResidue
BASP140
BTHR141
BASN245
BLYS290
BVAL292
BHOH684
CTHR253
CLYS254

site_idAF6
Number of Residues3
Detailsbinding site for residue EDO B 508
ChainResidue
BGLU218
BHOH751
DALA235

site_idAF7
Number of Residues5
Detailsbinding site for residue EDO B 509
ChainResidue
BLEU175
BTHR178
BTRP384
BASP391
BHOH631

site_idAF8
Number of Residues4
Detailsbinding site for residue EDO B 510
ChainResidue
BARG348
BLYS360
BHIS361
BHOH805

site_idAF9
Number of Residues6
Detailsbinding site for residue EDO B 511
ChainResidue
BASN115
BALA155
BASN161
BASN162
BARG335
BHOH709

site_idAG1
Number of Residues8
Detailsbinding site for residue EPE B 512
ChainResidue
BHIS105
BVAL106
BPHE107
BARG108
BGLU111
BGLN327
BLEU328
BGLN331

site_idAG2
Number of Residues3
Detailsbinding site for residue EDO B 513
ChainResidue
BASP374
BHIS378
BHOH672

site_idAG3
Number of Residues5
Detailsbinding site for residue EDO B 514
ChainResidue
BLYS284
BVAL287
BGLU288
BTHR383
BASP386

site_idAG4
Number of Residues7
Detailsbinding site for residue EDO B 515
ChainResidue
BHIS389
BPRO390
CTHR134
CPHE135
CLYS136
CASN251
CGLN256

site_idAG5
Number of Residues3
Detailsbinding site for residue EDO B 516
ChainResidue
BGLN210
BHOH651
BHOH710

site_idAG6
Number of Residues11
Detailsbinding site for residue E8H B 517
ChainResidue
BMET273
BLEU319
BASN321
BILE336
BMET357
BSER368
BGLN369
BPHE372
BHOH602
BHOH736
BHOH789

site_idAG7
Number of Residues2
Detailsbinding site for residue EDO C 501
ChainResidue
AEDO525
CGLU218

site_idAG8
Number of Residues5
Detailsbinding site for residue EDO C 502
ChainResidue
BPRO179
BHOH793
CLYS255
CSER259
CHOH625

site_idAG9
Number of Residues6
Detailsbinding site for residue ZN C 503
ChainResidue
CHIS164
CHIS200
CASP201
CASP318
CHOH617
CHOH693

site_idAH1
Number of Residues6
Detailsbinding site for residue MG C 504
ChainResidue
CASP201
CHOH617
CHOH621
CHOH687
CHOH711
CHOH723

site_idAH2
Number of Residues6
Detailsbinding site for residue EDO C 505
ChainResidue
AHOH620
CASN115
CARG116
CGLU150
CTYR153
CASN162

site_idAH3
Number of Residues4
Detailsbinding site for residue EDO C 506
ChainResidue
CSER208
CPRO356
CCYS358
CHOH724

site_idAH4
Number of Residues7
Detailsbinding site for residue EDO C 507
ChainResidue
CPHE238
CPHE249
CARG257
CARG261
CPG4519
CHOH603
CHOH634

site_idAH5
Number of Residues4
Detailsbinding site for residue EDO C 508
ChainResidue
CASP140
CTHR141
CASN245
CHOH616

site_idAH6
Number of Residues6
Detailsbinding site for residue EDO C 509
ChainResidue
CLEU175
CTHR178
CTRP384
CVAL388
CASP391
CILE395

site_idAH7
Number of Residues2
Detailsbinding site for residue EDO C 510
ChainResidue
CHIS154
CASP203

site_idAH8
Number of Residues7
Detailsbinding site for residue EPE C 511
ChainResidue
CHIS105
CPHE107
CARG108
CGLU111
CGLN327
CLEU328
CGLN331

site_idAH9
Number of Residues4
Detailsbinding site for residue EDO C 512
ChainResidue
CASN115
CALA155
CASN162
CARG335

site_idAI1
Number of Residues1
Detailsbinding site for residue EDO C 513
ChainResidue
CMET277

site_idAI2
Number of Residues5
Detailsbinding site for residue EDO C 514
ChainResidue
CGLN210
CHOH607
CHOH622
CHOH656
CHOH672

site_idAI3
Number of Residues7
Detailsbinding site for residue EDO C 515
ChainResidue
CPRO325
CLEU326
CASP401
CASN402
CHOH602
CHOH606
DARG330

site_idAI4
Number of Residues7
Detailsbinding site for residue EDO C 516
ChainResidue
APHE211
ALEU212
ASER217
APEG511
CHIS152
CGLU243
CHOH698

site_idAI5
Number of Residues3
Detailsbinding site for residue EDO C 517
ChainResidue
CGLU128
CHIS173
CSER177

site_idAI6
Number of Residues10
Detailsbinding site for residue E8H C 518
ChainResidue
CMET273
CASN321
CILE336
CMET357
CGLN369
CGLY371
CPHE372
CILE376
CHOH696
CHOH724

site_idAI7
Number of Residues10
Detailsbinding site for residue PG4 C 519
ChainResidue
CTYR223
CASN231
CLEU234
CALA235
CPHE238
CARG261
CEDO507
DLEU221
DMET222
DASN224

site_idAI8
Number of Residues5
Detailsbinding site for residue EDO D 501
ChainResidue
BGLU349
BARG350
DASP140
DTHR144
DMET147

site_idAI9
Number of Residues6
Detailsbinding site for residue EDO D 502
ChainResidue
AGLN258
BASN214
DSER294
DSER295
DHOH635
DHOH698

site_idAJ1
Number of Residues6
Detailsbinding site for residue ZN D 503
ChainResidue
DHIS164
DHIS200
DASP201
DASP318
DHOH610
DHOH734

site_idAJ2
Number of Residues6
Detailsbinding site for residue MG D 504
ChainResidue
DASP201
DHOH610
DHOH657
DHOH666
DHOH709
DHOH788

site_idAJ3
Number of Residues6
Detailsbinding site for residue EDO D 505
ChainResidue
ATHR134
APHE135
AASN251
AGLN256
AEDO508
DASP391

site_idAJ4
Number of Residues2
Detailsbinding site for residue EDO D 506
ChainResidue
DSER259
DTYR303

site_idAJ5
Number of Residues4
Detailsbinding site for residue EDO D 507
ChainResidue
DSER208
DPRO356
DHOH646
DHOH656

site_idAJ6
Number of Residues7
Detailsbinding site for residue EDO D 508
ChainResidue
DPHE238
DPHE249
DARG257
DARG261
DHOH630
DHOH677
DHOH749

site_idAJ7
Number of Residues9
Detailsbinding site for residue PEG D 509
ChainResidue
BASP156
BHOH773
DARG116
DGLU150
DASP151
DTYR153
DHIS154
DALA155
DHOH722

site_idAJ8
Number of Residues5
Detailsbinding site for residue EDO D 510
ChainResidue
AGLN256
ASER259
DGLU182
DHOH605
DHOH659

site_idAJ9
Number of Residues6
Detailsbinding site for residue EDO D 511
ChainResidue
BTHR215
BHOH637
DTHR148
DHIS152
DGLU243
DHOH606

site_idAK1
Number of Residues5
Detailsbinding site for residue EDO D 512
ChainResidue
CHOH632
CHOH651
DLYS262
DILE265
DASP266

site_idAK2
Number of Residues6
Detailsbinding site for residue EDO D 513
ChainResidue
DVAL174
DTHR178
DTRP384
DHOH602
DHOH620
DHOH694

site_idAK3
Number of Residues6
Detailsbinding site for residue EDO D 514
ChainResidue
DASP98
DLYS101
DTRP102
DGLY103
DHIS105
DHOH603

site_idAK4
Number of Residues4
Detailsbinding site for residue EDO D 515
ChainResidue
DASN115
DALA155
DASN162
DHOH663

site_idAK5
Number of Residues8
Detailsbinding site for residue EPE D 516
ChainResidue
DHIS105
DVAL106
DPHE107
DARG108
DGLU111
DGLN327
DLEU328
DGLN331

site_idAK6
Number of Residues4
Detailsbinding site for residue EDO D 517
ChainResidue
DASP266
DLEU269
DALA270
DGLN311

site_idAK7
Number of Residues9
Detailsbinding site for residue E8H D 518
ChainResidue
DMET273
DASN321
DILE336
DMET357
DSER368
DGLN369
DPHE372
DHOH762
DHOH821

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

数据于2024-04-24公开中

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