6HWO
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1335
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| A | 0007165 | biological_process | signal transduction |
| A | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| B | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| B | 0007165 | biological_process | signal transduction |
| B | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| C | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| C | 0007165 | biological_process | signal transduction |
| C | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| D | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| D | 0007165 | biological_process | signal transduction |
| D | 0008081 | molecular_function | phosphoric diester hydrolase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 501 |
| Chain | Residue |
| A | LYS262 |
| A | ASP266 |
| A | HOH619 |
| B | HOH640 |
| B | HOH645 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 502 |
| Chain | Residue |
| A | HOH651 |
| A | PHE238 |
| A | PHE249 |
| A | ARG257 |
| A | HOH620 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 503 |
| Chain | Residue |
| A | ASP156 |
| A | VAL157 |
| A | ALA158 |
| A | PRO205 |
| A | ARG346 |
| A | HOH602 |
| A | HOH662 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 504 |
| Chain | Residue |
| A | ASN251 |
| A | LEU252 |
| A | HOH694 |
| A | HOH712 |
| D | HOH655 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 505 |
| Chain | Residue |
| A | PHE135 |
| A | GLN256 |
| A | EDO506 |
| A | HOH707 |
| D | DMS502 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 506 |
| Chain | Residue |
| A | THR134 |
| A | LYS136 |
| A | EDO505 |
| D | ASP391 |
| D | EDO504 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 507 |
| Chain | Residue |
| A | LEU175 |
| A | THR178 |
| A | TRP384 |
| A | VAL388 |
| A | HOH671 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 508 |
| Chain | Residue |
| A | ASP266 |
| A | GLN311 |
| A | HOH625 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue PEG A 509 |
| Chain | Residue |
| A | LEU132 |
| A | LYS136 |
| A | ILE137 |
| A | HOH636 |
| A | HOH680 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue ZN A 510 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | HOH631 |
| A | HOH683 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 511 |
| Chain | Residue |
| A | HIS152 |
| A | GLU243 |
| C | THR215 |
| C | SER217 |
| C | ARG350 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 512 |
| Chain | Residue |
| A | THR186 |
| A | GLU189 |
| A | SER259 |
| A | MET263 |
| A | HOH607 |
| A | HOH614 |
| D | EDO501 |
| site_id | AD4 |
| Number of Residues | 10 |
| Details | binding site for residue FFZ A 513 |
| Chain | Residue |
| A | MET273 |
| A | LEU319 |
| A | ILE336 |
| A | MET337 |
| A | MET357 |
| A | SER368 |
| A | GLN369 |
| A | PHE372 |
| A | ILE376 |
| A | HOH657 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 514 |
| Chain | Residue |
| A | ASP201 |
| A | HOH610 |
| A | HOH631 |
| A | HOH638 |
| A | HOH640 |
| A | HOH690 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 515 |
| Chain | Residue |
| A | GLU243 |
| A | GLU244 |
| A | ASN245 |
| A | HOH616 |
| A | HOH642 |
| D | ARG257 |
| site_id | AD7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 516 |
| Chain | Residue |
| A | GLU218 |
| A | HOH682 |
| C | LYS239 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 517 |
| Chain | Residue |
| A | ASP140 |
| A | THR141 |
| A | ASN245 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 518 |
| Chain | Residue |
| A | GLN210 |
| A | ILE213 |
| A | HOH609 |
| A | HOH663 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 519 |
| Chain | Residue |
| A | THR289 |
| A | LYS291 |
| A | LEU298 |
| A | LEU299 |
| site_id | AE2 |
| Number of Residues | 8 |
| Details | binding site for residue EPE A 520 |
| Chain | Residue |
| A | HIS105 |
| A | VAL106 |
| A | PHE107 |
| A | ARG108 |
| A | GLU111 |
| A | LEU328 |
| A | GLN331 |
| A | HOH681 |
| site_id | AE3 |
| Number of Residues | 9 |
| Details | binding site for residue PEG A 521 |
| Chain | Residue |
| A | ASN115 |
| A | ARG116 |
| A | GLU150 |
| A | ASP151 |
| A | TYR153 |
| A | HIS154 |
| A | ALA155 |
| C | ASP156 |
| C | HOH619 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 501 |
| Chain | Residue |
| A | HOH608 |
| A | HOH668 |
| B | GLN210 |
| B | ILE213 |
| B | HOH640 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 502 |
| Chain | Residue |
| B | ASP334 |
| B | GLU338 |
| B | PHE341 |
| B | VAL365 |
| site_id | AE6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 503 |
| Chain | Residue |
| B | ALA183 |
| B | VAL184 |
| B | PHE185 |
| site_id | AE7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 504 |
| Chain | Residue |
| B | MET286 |
| B | THR289 |
| B | LYS290 |
| B | LYS291 |
| B | LEU299 |
| site_id | AE8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 505 |
| Chain | Residue |
| B | ASN115 |
| B | ALA155 |
| B | ASN162 |
| B | ILE163 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 506 |
| Chain | Residue |
| B | LEU175 |
| B | THR178 |
| B | TRP384 |
| B | VAL388 |
| B | ASP391 |
| site_id | AF1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 507 |
| Chain | Residue |
| B | ASP374 |
| B | HIS378 |
| B | HOH607 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 508 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | HOH612 |
| B | HOH691 |
| site_id | AF3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 509 |
| Chain | Residue |
| B | GLU218 |
| B | HOH650 |
| D | HIS152 |
| site_id | AF4 |
| Number of Residues | 4 |
| Details | binding site for residue DMS B 510 |
| Chain | Residue |
| B | ASN209 |
| B | GLN210 |
| B | HOH621 |
| B | HOH624 |
| site_id | AF5 |
| Number of Residues | 6 |
| Details | binding site for residue PEG B 511 |
| Chain | Residue |
| B | HIS152 |
| B | GLU243 |
| D | THR215 |
| D | SER217 |
| D | GLU218 |
| D | LEU219 |
| site_id | AF6 |
| Number of Residues | 9 |
| Details | binding site for residue FFZ B 512 |
| Chain | Residue |
| B | MET273 |
| B | LEU319 |
| B | ILE336 |
| B | MET357 |
| B | SER368 |
| B | GLN369 |
| B | GLY371 |
| B | PHE372 |
| B | HOH683 |
| site_id | AF7 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 513 |
| Chain | Residue |
| B | ASP201 |
| B | HOH612 |
| B | HOH625 |
| B | HOH648 |
| B | HOH659 |
| B | HOH701 |
| site_id | AF8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 514 |
| Chain | Residue |
| A | ASP225 |
| B | LYS262 |
| B | ASP266 |
| site_id | AF9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 515 |
| Chain | Residue |
| B | GLU218 |
| B | HOH636 |
| D | LYS239 |
| site_id | AG1 |
| Number of Residues | 7 |
| Details | binding site for residue EPE B 516 |
| Chain | Residue |
| B | HIS105 |
| B | VAL106 |
| B | PHE107 |
| B | ARG108 |
| B | GLU111 |
| B | LEU328 |
| B | GLN331 |
| site_id | AG2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 501 |
| Chain | Residue |
| A | GLU244 |
| C | ASN214 |
| C | ARG350 |
| C | MET352 |
| C | HOH601 |
| C | HOH710 |
| site_id | AG3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 502 |
| Chain | Residue |
| A | ARG342 |
| C | ASN115 |
| C | GLU150 |
| C | ASP151 |
| C | TYR153 |
| C | ASN162 |
| site_id | AG4 |
| Number of Residues | 8 |
| Details | binding site for residue EPE C 503 |
| Chain | Residue |
| C | HIS105 |
| C | PHE107 |
| C | ARG108 |
| C | GLU111 |
| C | GLN327 |
| C | LEU328 |
| C | GLN331 |
| C | HOH655 |
| site_id | AG5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 504 |
| Chain | Residue |
| C | LYS262 |
| C | ASP266 |
| D | ASN224 |
| D | SER226 |
| site_id | AG6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 505 |
| Chain | Residue |
| C | LEU269 |
| C | LYS275 |
| site_id | AG7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO C 506 |
| Chain | Residue |
| B | HIS389 |
| B | PRO390 |
| C | THR134 |
| C | PHE135 |
| C | LYS136 |
| C | ASN251 |
| C | GLN256 |
| site_id | AG8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 507 |
| Chain | Residue |
| C | HIS154 |
| C | ASP203 |
| site_id | AG9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 508 |
| Chain | Residue |
| C | ALA158 |
| C | PRO205 |
| C | ARG342 |
| C | ARG346 |
| C | HOH607 |
| site_id | AH1 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 509 |
| Chain | Residue |
| C | HIS164 |
| C | HIS200 |
| C | ASP201 |
| C | ASP318 |
| C | HOH617 |
| C | HOH680 |
| site_id | AH2 |
| Number of Residues | 9 |
| Details | binding site for residue FFZ C 510 |
| Chain | Residue |
| C | MET273 |
| C | LEU319 |
| C | ASN321 |
| C | ILE336 |
| C | SER368 |
| C | GLN369 |
| C | PHE372 |
| C | HOH672 |
| C | HOH691 |
| site_id | AH3 |
| Number of Residues | 5 |
| Details | binding site for residue PEG C 511 |
| Chain | Residue |
| C | ILE213 |
| C | ASP225 |
| C | HOH700 |
| D | GLN258 |
| D | LYS262 |
| site_id | AH4 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 512 |
| Chain | Residue |
| C | ASP201 |
| C | HOH617 |
| C | HOH618 |
| C | HOH661 |
| C | HOH669 |
| C | HOH701 |
| site_id | AH5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 513 |
| Chain | Residue |
| A | ASP140 |
| A | ILE143 |
| C | GLU349 |
| site_id | AH6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 514 |
| Chain | Residue |
| B | LYS290 |
| B | VAL292 |
| C | THR253 |
| C | LYS254 |
| C | HOH612 |
| site_id | AH7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 501 |
| Chain | Residue |
| A | LEU188 |
| A | LYS255 |
| A | GLN256 |
| A | EDO512 |
| D | GLU182 |
| site_id | AH8 |
| Number of Residues | 4 |
| Details | binding site for residue DMS D 502 |
| Chain | Residue |
| A | EDO505 |
| D | SER177 |
| D | PRO179 |
| D | GLU182 |
| site_id | AH9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 503 |
| Chain | Residue |
| B | SER217 |
| D | THR148 |
| D | HIS152 |
| D | GLU243 |
| site_id | AI1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 504 |
| Chain | Residue |
| A | THR134 |
| A | ASN251 |
| A | GLN256 |
| A | EDO506 |
| D | PRO179 |
| D | ASP391 |
| site_id | AI2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 505 |
| Chain | Residue |
| D | LEU175 |
| D | THR178 |
| D | ASP391 |
| D | HOH602 |
| D | HOH606 |
| site_id | AI3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 506 |
| Chain | Residue |
| D | LEU181 |
| D | ALA183 |
| D | VAL184 |
| D | PHE185 |
| D | HOH616 |
| D | HOH697 |
| D | HOH735 |
| site_id | AI4 |
| Number of Residues | 4 |
| Details | binding site for residue DMS D 507 |
| Chain | Residue |
| D | GLU150 |
| D | ASP151 |
| D | TYR153 |
| D | ASN162 |
| site_id | AI5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 508 |
| Chain | Residue |
| D | ASN100 |
| D | LYS101 |
| D | TRP102 |
| site_id | AI6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 509 |
| Chain | Residue |
| D | HIS123 |
| D | HOH764 |
| site_id | AI7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 510 |
| Chain | Residue |
| D | ASP156 |
| D | VAL157 |
| D | ALA158 |
| D | ARG342 |
| D | HOH612 |
| D | HOH652 |
| D | HOH670 |
| site_id | AI8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 511 |
| Chain | Residue |
| D | THR134 |
| D | ASN251 |
| D | GLN256 |
| site_id | AI9 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 512 |
| Chain | Residue |
| D | HIS164 |
| D | HIS200 |
| D | ASP201 |
| D | ASP318 |
| D | HOH638 |
| D | HOH706 |
| site_id | AJ1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 513 |
| Chain | Residue |
| D | ASP98 |
| D | TRP102 |
| site_id | AJ2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 514 |
| Chain | Residue |
| D | ASP266 |
| D | GLN311 |
| D | HOH632 |
| site_id | AJ3 |
| Number of Residues | 9 |
| Details | binding site for residue FFZ D 515 |
| Chain | Residue |
| D | MET273 |
| D | ASN321 |
| D | ILE336 |
| D | SER368 |
| D | GLN369 |
| D | GLY371 |
| D | PHE372 |
| D | HOH659 |
| D | HOH730 |
| site_id | AJ4 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 516 |
| Chain | Residue |
| D | ASP201 |
| D | HOH638 |
| D | HOH647 |
| D | HOH658 |
| D | HOH679 |
| D | HOH680 |
| site_id | AJ5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 517 |
| Chain | Residue |
| C | ASN231 |
| C | LEU234 |
| C | HOH624 |
| D | LEU221 |
| D | MET222 |
| D | ASN224 |
| D | HOH617 |
| site_id | AJ6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 518 |
| Chain | Residue |
| B | GLU349 |
| B | ARG350 |
| D | ASP140 |
| D | ILE143 |
| D | THR144 |
| site_id | AJ7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 519 |
| Chain | Residue |
| D | PHE238 |
| D | PHE249 |
| D | ARG257 |
| D | ARG261 |
| D | HOH660 |
| D | HOH695 |
| site_id | AJ8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 520 |
| Chain | Residue |
| D | THR289 |
| D | LYS290 |
| D | LYS291 |
| D | LEU298 |
| D | LEU299 |
| D | HOH601 |
| site_id | AJ9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 521 |
| Chain | Residue |
| D | THR186 |
| D | GLU189 |
| D | SER259 |
| D | MET263 |
| site_id | AK1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 522 |
| Chain | Residue |
| D | ALA183 |
| D | VAL184 |
| site_id | AK2 |
| Number of Residues | 8 |
| Details | binding site for residue EPE D 523 |
| Chain | Residue |
| D | HIS105 |
| D | VAL106 |
| D | PHE107 |
| D | ARG108 |
| D | GLU111 |
| D | GLN327 |
| D | LEU328 |
| D | GLN331 |
| site_id | AK3 |
| Number of Residues | 3 |
| Details | binding site for residue PEG D 524 |
| Chain | Residue |
| D | LYS136 |
| D | ILE137 |
| D | VAL139 |
Functional Information from PROSITE/UniProt
| site_id | PS00126 |
| Number of Residues | 12 |
| Details | PDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDVdHpGvsNqF |
| Chain | Residue | Details |
| A | HIS200-PHE211 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"Q07343","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)"} |
| Chain | Residue | Details |
