6RCW
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053
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 | 6 |
| Details | binding site for residue ZN A 501 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | HOH650 |
| A | HOH711 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 502 |
| Chain | Residue |
| A | HOH650 |
| A | HOH694 |
| A | HOH730 |
| A | ASP201 |
| A | HOH629 |
| A | HOH645 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 503 |
| Chain | Residue |
| A | SER208 |
| A | PRO356 |
| A | CYS358 |
| A | HOH664 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 504 |
| Chain | Residue |
| A | ASN115 |
| A | ALA155 |
| A | VAL157 |
| A | ASN161 |
| A | ASN162 |
| A | HOH627 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 505 |
| Chain | Residue |
| A | THR186 |
| A | GLU189 |
| A | SER259 |
| A | MET263 |
| A | HOH601 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 506 |
| Chain | Residue |
| A | SER226 |
| A | ASN231 |
| B | HOH659 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 507 |
| Chain | Residue |
| A | GLU218 |
| A | EDO509 |
| A | HOH603 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 508 |
| Chain | Residue |
| A | LYS275 |
| A | HOH624 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 509 |
| Chain | Residue |
| A | GLU218 |
| A | EDO507 |
| A | HOH603 |
| C | HIS152 |
| C | HOH603 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 510 |
| Chain | Residue |
| A | PHE238 |
| A | PHE249 |
| A | ARG257 |
| A | ARG261 |
| A | HOH636 |
| A | HOH637 |
| A | HOH707 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 511 |
| Chain | Residue |
| A | LYS262 |
| A | ASP266 |
| A | HOH611 |
| B | HOH637 |
| B | HOH657 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 512 |
| Chain | Residue |
| A | MET286 |
| A | THR289 |
| A | LYS290 |
| A | LYS291 |
| A | LEU298 |
| A | LEU299 |
| site_id | AD4 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 513 |
| Chain | Residue |
| A | GLU243 |
| A | GLU244 |
| A | ASN245 |
| A | HOH623 |
| A | HOH625 |
| A | HOH641 |
| A | HOH727 |
| D | ARG257 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 514 |
| Chain | Residue |
| A | THR148 |
| A | HIS152 |
| A | GLU243 |
| C | THR215 |
| C | ARG350 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue PEG A 515 |
| Chain | Residue |
| A | VAL174 |
| A | LEU175 |
| A | THR178 |
| A | TRP384 |
| A | VAL388 |
| A | ASP391 |
| A | ILE395 |
| site_id | AD7 |
| Number of Residues | 10 |
| Details | binding site for residue DTT A 516 |
| Chain | Residue |
| A | GLU150 |
| A | ASP151 |
| A | TYR153 |
| A | HIS154 |
| A | ALA155 |
| A | HOH609 |
| A | HOH658 |
| C | ASP156 |
| C | HOH670 |
| C | HOH693 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 501 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | HOH612 |
| B | HOH703 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 502 |
| Chain | Residue |
| B | HOH667 |
| B | ASP201 |
| B | HOH601 |
| B | HOH612 |
| B | HOH644 |
| B | HOH645 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 503 |
| Chain | Residue |
| B | SER208 |
| B | PHE340 |
| B | PRO356 |
| B | MET357 |
| B | HOH629 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 504 |
| Chain | Residue |
| B | GLU218 |
| B | HOH622 |
| D | LYS239 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 505 |
| Chain | Residue |
| A | GLN258 |
| B | GLN210 |
| B | ASN214 |
| B | EDO510 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 506 |
| Chain | Residue |
| B | ASN115 |
| B | ALA155 |
| B | ASN161 |
| B | ASN162 |
| B | ARG335 |
| site_id | AE5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 507 |
| Chain | Residue |
| A | ASN224 |
| B | LYS262 |
| B | ASP266 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 508 |
| Chain | Residue |
| B | HIS154 |
| B | ASP203 |
| B | LEU219 |
| B | HIS232 |
| site_id | AE7 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 509 |
| Chain | Residue |
| B | VAL292 |
| site_id | AE8 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 510 |
| Chain | Residue |
| B | PHE211 |
| B | ASN214 |
| B | GLU347 |
| B | MET352 |
| B | GLU353 |
| B | SER355 |
| B | EDO505 |
| site_id | AE9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 511 |
| Chain | Residue |
| B | GLN210 |
| B | HOH614 |
| B | HOH635 |
| B | HOH713 |
| site_id | AF1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 512 |
| Chain | Residue |
| B | THR289 |
| B | LYS291 |
| B | LEU299 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue EPE B 513 |
| Chain | Residue |
| B | ASP140 |
| B | THR141 |
| B | ASN245 |
| B | HOH670 |
| C | THR253 |
| C | LYS254 |
| site_id | AF3 |
| Number of Residues | 12 |
| Details | binding site for residue JX2 B 514 |
| Chain | Residue |
| B | HIS160 |
| B | MET273 |
| B | ASP318 |
| B | LEU319 |
| B | ASN321 |
| B | MET357 |
| B | SER368 |
| B | GLN369 |
| B | PHE372 |
| B | HOH667 |
| B | HOH703 |
| B | HOH705 |
| site_id | AF4 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 501 |
| Chain | Residue |
| C | HIS164 |
| C | HIS200 |
| C | ASP201 |
| C | ASP318 |
| C | HOH604 |
| C | HOH710 |
| site_id | AF5 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 502 |
| Chain | Residue |
| C | ASP201 |
| C | HOH604 |
| C | HOH622 |
| C | HOH649 |
| C | HOH651 |
| C | HOH706 |
| site_id | AF6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 503 |
| Chain | Residue |
| C | SER208 |
| C | PRO356 |
| C | CYS358 |
| site_id | AF7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 504 |
| Chain | Residue |
| C | ARG257 |
| C | HOH612 |
| C | HOH689 |
| site_id | AF8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 505 |
| Chain | Residue |
| C | LEU188 |
| C | LYS255 |
| C | SER259 |
| C | HOH607 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 506 |
| Chain | Residue |
| C | LEU175 |
| C | THR178 |
| C | TRP384 |
| C | VAL388 |
| C | ASP391 |
| site_id | AG1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 507 |
| Chain | Residue |
| C | ARG330 |
| C | GLU366 |
| C | TYR406 |
| C | THR409 |
| D | PRO411 |
| site_id | AG2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 508 |
| Chain | Residue |
| C | ASP203 |
| C | LEU219 |
| site_id | AG3 |
| Number of Residues | 9 |
| Details | binding site for residue EPE C 509 |
| Chain | Residue |
| C | HIS105 |
| C | VAL106 |
| C | PHE107 |
| C | ARG108 |
| C | GLU111 |
| C | GLN327 |
| C | LEU328 |
| C | GLN331 |
| C | HOH683 |
| site_id | AG4 |
| Number of Residues | 15 |
| Details | binding site for residue JX2 C 510 |
| Chain | Residue |
| C | HIS160 |
| C | MET273 |
| C | ASP318 |
| C | LEU319 |
| C | ASN321 |
| C | ILE336 |
| C | MET357 |
| C | SER368 |
| C | GLN369 |
| C | GLY371 |
| C | PHE372 |
| C | ILE376 |
| C | HOH672 |
| C | HOH706 |
| C | HOH710 |
| site_id | AG5 |
| Number of Residues | 10 |
| Details | binding site for residue DTT D 501 |
| Chain | Residue |
| B | ASP156 |
| D | GLU150 |
| D | ASP151 |
| D | HIS152 |
| D | TYR153 |
| D | HIS154 |
| D | ALA155 |
| D | EDO509 |
| D | HOH610 |
| D | HOH735 |
| site_id | AG6 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 502 |
| Chain | Residue |
| D | HIS164 |
| D | HIS200 |
| D | ASP201 |
| D | ASP318 |
| D | HOH619 |
| D | HOH736 |
| site_id | AG7 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 503 |
| Chain | Residue |
| D | ASP201 |
| D | HOH619 |
| D | HOH630 |
| D | HOH672 |
| D | HOH698 |
| D | HOH744 |
| site_id | AG8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 504 |
| Chain | Residue |
| D | PRO179 |
| D | ASP391 |
| site_id | AG9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 505 |
| Chain | Residue |
| D | SER294 |
| D | HOH617 |
| D | HOH624 |
| site_id | AH1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 506 |
| Chain | Residue |
| D | SER208 |
| D | PRO356 |
| D | MET357 |
| D | CYS358 |
| D | JX2515 |
| D | HOH647 |
| site_id | AH2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 507 |
| Chain | Residue |
| D | PHE238 |
| D | PHE249 |
| D | ARG257 |
| D | ARG261 |
| D | HOH621 |
| D | HOH632 |
| site_id | AH3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 508 |
| Chain | Residue |
| C | HOH684 |
| C | HOH702 |
| D | LYS262 |
| D | ASP266 |
| D | HOH663 |
| site_id | AH4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 509 |
| Chain | Residue |
| D | ASN115 |
| D | ALA155 |
| D | ASN162 |
| D | ILE163 |
| D | DTT501 |
| D | HOH615 |
| site_id | AH5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 510 |
| Chain | Residue |
| D | LEU175 |
| D | THR178 |
| D | TRP384 |
| D | VAL388 |
| D | ASP391 |
| D | HOH652 |
| site_id | AH6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 511 |
| Chain | Residue |
| C | ASN214 |
| C | GLU353 |
| C | HOH618 |
| D | GLN258 |
| site_id | AH7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 512 |
| Chain | Residue |
| B | THR215 |
| D | THR148 |
| D | HIS152 |
| D | GLU243 |
| site_id | AH8 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 513 |
| Chain | Residue |
| D | GLU182 |
| site_id | AH9 |
| Number of Residues | 1 |
| Details | binding site for residue PEG D 514 |
| Chain | Residue |
| D | HIS123 |
| site_id | AI1 |
| Number of Residues | 13 |
| Details | binding site for residue JX2 D 515 |
| Chain | Residue |
| D | HIS160 |
| D | MET273 |
| D | ASP318 |
| D | LEU319 |
| D | ASN321 |
| D | MET357 |
| D | SER368 |
| D | GLN369 |
| D | PHE372 |
| D | EDO506 |
| D | HOH727 |
| D | HOH736 |
| D | HOH744 |
| site_id | AI2 |
| Number of Residues | 4 |
| Details | binding site for residue PEG D 516 |
| Chain | Residue |
| D | PRO325 |
| D | LEU326 |
| D | ASP401 |
| D | ASN402 |
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 | ACT_SITE: Proton donor => ECO:0000250|UniProtKB:Q07343 |
| Chain | Residue | Details |
| A | HIS160 | |
| B | HIS160 | |
| C | HIS160 | |
| D | HIS160 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7 |
| Chain | Residue | Details |
| A | HIS160 | |
| D | HIS160 | |
| D | ASN321 | |
| D | GLN369 | |
| A | ASN321 | |
| A | GLN369 | |
| B | HIS160 | |
| B | ASN321 | |
| B | GLN369 | |
| C | HIS160 | |
| C | ASN321 | |
| C | GLN369 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: 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 |
| Chain | Residue | Details |
| A | HIS164 | |
| B | HIS164 | |
| C | HIS164 | |
| D | HIS164 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: 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 |
| Chain | Residue | Details |
| A | HIS200 | |
| A | ASP318 | |
| B | HIS200 | |
| B | ASP318 | |
| C | HIS200 | |
| C | ASP318 | |
| D | HIS200 | |
| D | ASP318 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW |
| Chain | Residue | Details |
| A | ASP201 | |
| A | PHE372 | |
| B | ASP201 | |
| B | PHE372 | |
| C | ASP201 | |
| C | PHE372 | |
| D | ASP201 | |
| D | PHE372 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) |
| Chain | Residue | Details |
| A | LYS85 | |
| B | LYS85 | |
| C | LYS85 | |
| D | LYS85 |
