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6FEB

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1086

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
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue EDO A 501
ChainResidue
ALYS262
AASP266
BHOH611
BHOH614

site_idAC2
Number of Residues5
Detailsbinding site for residue EDO A 502
ChainResidue
ASER208
ASER355
APRO356
ACYS358
AHOH655

site_idAC3
Number of Residues2
Detailsbinding site for residue EDO A 503
ChainResidue
AGLU182
BLYS255

site_idAC4
Number of Residues6
Detailsbinding site for residue EDO A 504
ChainResidue
ALEU175
ATHR178
ATRP384
AASP391
AILE395
AHOH613

site_idAC5
Number of Residues4
Detailsbinding site for residue EDO A 505
ChainResidue
AASP391
BTHR134
BASN251
BGLN256

site_idAC6
Number of Residues4
Detailsbinding site for residue EDO A 506
ChainResidue
AASP247
APHE249
AGLN250
AARG257

site_idAC7
Number of Residues4
Detailsbinding site for residue EDO A 507
ChainResidue
AGLN210
AHOH625
AHOH631
AHOH653

site_idAC8
Number of Residues5
Detailsbinding site for residue EDO A 508
ChainResidue
AASP266
ALEU269
ALYS275
AGLN311
AHOH612

site_idAC9
Number of Residues2
Detailsbinding site for residue EDO A 509
ChainResidue
AASN278
AASP282

site_idAD1
Number of Residues1
Detailsbinding site for residue EDO A 510
ChainResidue
AASP374

site_idAD2
Number of Residues10
Detailsbinding site for residue D5Z A 511
ChainResidue
AMET273
AASN321
AILE336
AMET337
APRO356
AMET357
AGLN369
APHE372
AILE376
AHOH683

site_idAD3
Number of Residues9
Detailsbinding site for residue D5Z A 512
ChainResidue
AGLN127
ALEU132
ALYS133
ALYS136
AILE137
AGLU288
ATHR289
AVAL292
ATHR293

site_idAD4
Number of Residues6
Detailsbinding site for residue MG A 513
ChainResidue
AASP201
AHOH621
AHOH622
AHOH648
AHOH665
AHOH728

site_idAD5
Number of Residues6
Detailsbinding site for residue ZN A 514
ChainResidue
AHIS164
AHIS200
AASP201
AASP318
AHOH621
AHOH693

site_idAD6
Number of Residues7
Detailsbinding site for residue EPE A 515
ChainResidue
AHIS105
AVAL106
APHE107
AARG108
AGLU111
ALEU328
AGLN331

site_idAD7
Number of Residues4
Detailsbinding site for residue EDO A 516
ChainResidue
AASN231
AHOH688
AHOH714
BASN231

site_idAD8
Number of Residues4
Detailsbinding site for residue EDO B 501
ChainResidue
AHOH614
AHOH636
BLYS262
BASP266

site_idAD9
Number of Residues4
Detailsbinding site for residue EDO B 502
ChainResidue
BSER208
BSER355
BPRO356
BCYS358

site_idAE1
Number of Residues6
Detailsbinding site for residue EDO B 503
ChainResidue
APRO179
AALA180
AGLU182
BTHR253
BLYS254
BLYS255

site_idAE2
Number of Residues5
Detailsbinding site for residue EDO B 504
ChainResidue
BHIS152
BTHR215
BSER217
BGLU243
BARG350

site_idAE3
Number of Residues4
Detailsbinding site for residue EDO B 505
ChainResidue
BASP203
BPRO205
BLEU219
BHIS154

site_idAE4
Number of Residues4
Detailsbinding site for residue EDO B 506
ChainResidue
BASN115
BGLU150
BTYR153
BASN162

site_idAE5
Number of Residues6
Detailsbinding site for residue EDO B 507
ChainResidue
BLEU175
BTHR178
BTRP384
BVAL388
BASP391
BILE395

site_idAE6
Number of Residues9
Detailsbinding site for residue D5Z B 508
ChainResidue
BMET273
BLEU319
BASN321
BILE336
BMET357
BGLN369
BPHE372
BILE376
BHOH667

site_idAE7
Number of Residues6
Detailsbinding site for residue MG B 509
ChainResidue
BASP201
BHOH603
BHOH628
BHOH632
BHOH664
BHOH687

site_idAE8
Number of Residues6
Detailsbinding site for residue ZN B 510
ChainResidue
BHIS164
BHIS200
BASP201
BASP318
BHOH603
BHOH672

site_idAE9
Number of Residues7
Detailsbinding site for residue EPE B 511
ChainResidue
BHIS105
BVAL106
BPHE107
BARG108
BGLU111
BLEU328
BGLN331

site_idAF1
Number of Residues3
Detailsbinding site for residue EDO B 512
ChainResidue
BPHE238
BARG257
BHOH636

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 Residues2
DetailsACT_SITE: Proton donor => ECO:0000250|UniProtKB:Q07343
ChainResidueDetails
AHIS160
BHIS160

site_idSWS_FT_FI2
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7
ChainResidueDetails
AHIS160
AASN321
AGLN369
BHIS160
BASN321
BGLN369

site_idSWS_FT_FI3
Number of Residues2
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

site_idSWS_FT_FI4
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:1XOR, ECO:0007744|PDB:2PW3
ChainResidueDetails
AHIS200
AASP318
BHIS200
BASP318

site_idSWS_FT_FI5
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW
ChainResidueDetails
AASP201
APHE372
BASP201
BPHE372

site_idSWS_FT_FI6
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)
ChainResidueDetails
ALYS85
BLYS85

224004

PDB entries from 2024-08-21

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