6IBF
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417
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 | 7 |
| Details | binding site for residue ZN A 501 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | MG502 |
| A | HOH611 |
| A | HOH639 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 502 |
| Chain | Residue |
| A | HOH606 |
| A | HOH608 |
| A | HOH611 |
| A | HOH646 |
| A | HOH665 |
| A | ASP201 |
| A | ZN501 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 503 |
| Chain | Residue |
| A | ASN115 |
| A | ALA155 |
| A | ASN162 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 504 |
| Chain | Residue |
| A | THR186 |
| A | LEU188 |
| A | GLU189 |
| A | SER259 |
| A | MET263 |
| A | HOH620 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 505 |
| Chain | Residue |
| A | LYS262 |
| A | ASP266 |
| B | HOH611 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 506 |
| Chain | Residue |
| A | LEU175 |
| A | THR178 |
| A | TRP384 |
| A | ASP391 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 507 |
| Chain | Residue |
| A | GLU218 |
| C | VAL236 |
| C | LYS239 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 508 |
| Chain | Residue |
| A | ASP266 |
| A | LEU269 |
| A | LYS275 |
| A | GLN311 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 509 |
| Chain | Residue |
| A | THR148 |
| A | HIS152 |
| A | GLU243 |
| C | SER217 |
| C | ARG350 |
| C | EDO507 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue EPE A 510 |
| Chain | Residue |
| A | HIS105 |
| A | VAL106 |
| A | PHE107 |
| A | ARG108 |
| A | GLU111 |
| A | LEU328 |
| A | GLN331 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 511 |
| Chain | Residue |
| A | ASP140 |
| A | ASN245 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 512 |
| Chain | Residue |
| A | ARG116 |
| A | GLU150 |
| A | ASP151 |
| A | TYR153 |
| A | ALA155 |
| C | ARG346 |
| site_id | AD4 |
| Number of Residues | 14 |
| Details | binding site for residue 4I7 A 513 |
| Chain | Residue |
| A | MET273 |
| A | LEU319 |
| A | THR333 |
| A | ILE336 |
| A | MET337 |
| A | PHE340 |
| A | PRO356 |
| A | MET357 |
| A | SER368 |
| A | GLN369 |
| A | PHE372 |
| A | ILE376 |
| A | HOH638 |
| A | HOH639 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 501 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | HOH603 |
| B | HOH673 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 502 |
| Chain | Residue |
| B | ASP201 |
| B | HOH603 |
| B | HOH617 |
| B | HOH650 |
| B | HOH653 |
| B | HOH659 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 503 |
| Chain | Residue |
| B | SER208 |
| B | PHE340 |
| B | PRO356 |
| B | HOH607 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 504 |
| Chain | Residue |
| B | ASN115 |
| B | ALA155 |
| B | ASN161 |
| B | ASN162 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 505 |
| Chain | Residue |
| A | ASN224 |
| A | ASP225 |
| B | LYS262 |
| B | ASP266 |
| site_id | AE1 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 506 |
| Chain | Residue |
| B | VAL292 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 507 |
| Chain | Residue |
| B | HOH630 |
| D | THR144 |
| B | GLU349 |
| B | ARG350 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 508 |
| Chain | Residue |
| B | ALA183 |
| B | VAL184 |
| B | PHE185 |
| site_id | AE4 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 509 |
| Chain | Residue |
| B | GLN256 |
| site_id | AE5 |
| Number of Residues | 7 |
| Details | binding site for residue EPE B 510 |
| Chain | Residue |
| B | HIS105 |
| B | VAL106 |
| B | PHE107 |
| B | ARG108 |
| B | GLU111 |
| B | LEU328 |
| B | GLN331 |
| site_id | AE6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 511 |
| Chain | Residue |
| B | PHE211 |
| B | THR215 |
| B | SER217 |
| B | ARG350 |
| D | HIS152 |
| D | GLU243 |
| site_id | AE7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 512 |
| Chain | Residue |
| B | HIS152 |
| B | GLU243 |
| D | THR215 |
| D | SER217 |
| D | ARG350 |
| site_id | AE8 |
| Number of Residues | 14 |
| Details | binding site for residue 4I7 B 513 |
| Chain | Residue |
| B | MET273 |
| B | ASP318 |
| B | LEU319 |
| B | ASN321 |
| B | ILE336 |
| B | MET337 |
| B | PHE340 |
| B | MET357 |
| B | SER368 |
| B | GLN369 |
| B | PHE372 |
| B | HOH671 |
| B | HOH673 |
| B | HOH685 |
| site_id | AE9 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 501 |
| Chain | Residue |
| C | HIS164 |
| C | HIS200 |
| C | ASP201 |
| C | ASP318 |
| C | HOH615 |
| C | HOH638 |
| site_id | AF1 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 502 |
| Chain | Residue |
| C | ASP201 |
| C | HOH615 |
| C | HOH627 |
| C | HOH629 |
| C | HOH630 |
| C | HOH678 |
| site_id | AF2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 503 |
| Chain | Residue |
| C | LEU188 |
| C | LYS255 |
| C | SER259 |
| site_id | AF3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO C 504 |
| Chain | Residue |
| C | VAL174 |
| C | LEU175 |
| C | THR178 |
| C | TRP384 |
| C | ASP391 |
| C | ALA392 |
| C | ILE395 |
| site_id | AF4 |
| Number of Residues | 9 |
| Details | binding site for residue EPE C 505 |
| Chain | Residue |
| C | HIS105 |
| C | VAL106 |
| C | PHE107 |
| C | ARG108 |
| C | GLU111 |
| C | GLN327 |
| C | LEU328 |
| C | GLN331 |
| C | HOH647 |
| site_id | AF5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 506 |
| Chain | Residue |
| A | SER217 |
| A | ARG350 |
| C | THR148 |
| C | HIS152 |
| C | GLU243 |
| site_id | AF6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 507 |
| Chain | Residue |
| A | ASP151 |
| A | EDO509 |
| C | ARG346 |
| site_id | AF7 |
| Number of Residues | 11 |
| Details | binding site for residue 4I7 C 508 |
| Chain | Residue |
| C | MET273 |
| C | LEU319 |
| C | ASN321 |
| C | ILE336 |
| C | MET337 |
| C | PHE340 |
| C | MET357 |
| C | SER368 |
| C | GLN369 |
| C | PHE372 |
| C | ILE376 |
| site_id | AF8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 509 |
| Chain | Residue |
| C | ASP98 |
| C | TRP102 |
| site_id | AF9 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 501 |
| Chain | Residue |
| D | HIS164 |
| D | HIS200 |
| D | ASP201 |
| D | ASP318 |
| D | HOH608 |
| D | HOH669 |
| site_id | AG1 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 502 |
| Chain | Residue |
| D | ASP201 |
| D | HOH608 |
| D | HOH640 |
| D | HOH641 |
| D | HOH656 |
| D | HOH673 |
| site_id | AG2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 503 |
| Chain | Residue |
| D | PHE340 |
| D | PRO356 |
| D | CYS358 |
| D | 4I7520 |
| D | HOH678 |
| site_id | AG3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 504 |
| Chain | Residue |
| D | LYS262 |
| D | ASP266 |
| D | HOH629 |
| site_id | AG4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 505 |
| Chain | Residue |
| D | ASN115 |
| D | ALA155 |
| D | ASN161 |
| D | ASN162 |
| D | ILE163 |
| D | HOH638 |
| site_id | AG5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 507 |
| Chain | Residue |
| D | THR186 |
| D | GLU189 |
| D | SER259 |
| site_id | AG6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 508 |
| Chain | Residue |
| D | THR134 |
| D | ASN251 |
| D | GLN256 |
| site_id | AG7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 509 |
| Chain | Residue |
| D | SER259 |
| D | LYS262 |
| D | TYR303 |
| site_id | AG8 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 510 |
| Chain | Residue |
| D | GLU182 |
| site_id | AG9 |
| Number of Residues | 7 |
| Details | binding site for residue PEG D 511 |
| Chain | Residue |
| D | VAL174 |
| D | LEU175 |
| D | THR178 |
| D | TRP384 |
| D | ASP391 |
| D | PEG512 |
| D | HOH633 |
| site_id | AH1 |
| Number of Residues | 3 |
| Details | binding site for residue PEG D 512 |
| Chain | Residue |
| D | PRO179 |
| D | ASP391 |
| D | PEG511 |
| site_id | AH2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 513 |
| Chain | Residue |
| D | GLU128 |
| D | SER177 |
| site_id | AH3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 514 |
| Chain | Residue |
| D | ASP98 |
| D | TRP102 |
| D | GLY103 |
| D | HOH631 |
| D | HOH636 |
| site_id | AH4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 515 |
| Chain | Residue |
| C | ASN231 |
| C | LEU234 |
| D | LEU221 |
| D | MET222 |
| D | ASN224 |
| D | HOH607 |
| site_id | AH5 |
| Number of Residues | 7 |
| Details | binding site for residue EPE D 516 |
| Chain | Residue |
| D | HIS105 |
| D | VAL106 |
| D | PHE107 |
| D | ARG108 |
| D | GLU111 |
| D | LEU328 |
| D | GLN331 |
| site_id | AH6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 517 |
| Chain | Residue |
| D | GLU218 |
| D | MET222 |
| site_id | AH7 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 518 |
| Chain | Residue |
| D | HOH630 |
| site_id | AH8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 519 |
| Chain | Residue |
| D | PHE238 |
| D | ARG257 |
| D | HOH626 |
| site_id | AH9 |
| Number of Residues | 12 |
| Details | binding site for residue 4I7 D 520 |
| Chain | Residue |
| D | MET273 |
| D | LEU319 |
| D | ASN321 |
| D | ILE336 |
| D | MET337 |
| D | PHE340 |
| D | MET357 |
| D | SER368 |
| D | GLN369 |
| D | PHE372 |
| D | EDO503 |
| D | HOH691 |
| site_id | AI1 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 521 |
| Chain | Residue |
| D | GLU218 |
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 |
