5K32
PDE4D crystal structure in complex with small molecule inhibitor
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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | binding site for residue ZN A 1001 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | MG1002 |
| A | HOH1154 |
| A | HOH1214 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 1002 |
| Chain | Residue |
| A | HOH1141 |
| A | HOH1169 |
| A | HOH1200 |
| A | HOH1214 |
| A | HOH1218 |
| A | ASP201 |
| A | ZN1001 |
| site_id | AC3 |
| Number of Residues | 13 |
| Details | binding site for residue 6Q2 A 1003 |
| Chain | Residue |
| A | TYR159 |
| A | THR271 |
| A | MET273 |
| A | ASP318 |
| A | ASN321 |
| A | THR333 |
| A | GLN369 |
| A | PHE372 |
| A | EDO1010 |
| A | EDO1011 |
| A | EDO1013 |
| A | HOH1122 |
| A | HOH1186 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 1004 |
| Chain | Residue |
| A | LYS262 |
| A | ILE265 |
| A | ASP266 |
| A | HOH1108 |
| B | ASN224 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 1005 |
| Chain | Residue |
| A | ASN209 |
| A | GLN210 |
| A | HOH1107 |
| A | HOH1133 |
| A | HOH1162 |
| A | HOH1182 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 1006 |
| Chain | Residue |
| A | GLU150 |
| A | TYR153 |
| A | ASN162 |
| A | EDO1007 |
| A | HOH1125 |
| A | HOH1151 |
| A | HOH1314 |
| B | GLN407 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 1007 |
| Chain | Residue |
| A | ASN115 |
| A | ALA155 |
| A | ASN161 |
| A | ASN162 |
| A | ILE163 |
| A | EDO1006 |
| A | HOH1151 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 1008 |
| Chain | Residue |
| A | VAL174 |
| A | SER177 |
| A | THR178 |
| A | ASP391 |
| A | HOH1112 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 1009 |
| Chain | Residue |
| A | PHE238 |
| A | ARG257 |
| A | HOH1193 |
| site_id | AD1 |
| Number of Residues | 10 |
| Details | binding site for residue EDO A 1010 |
| Chain | Residue |
| A | HIS204 |
| A | GLY206 |
| A | VAL207 |
| A | SER208 |
| A | GLU339 |
| A | PHE340 |
| A | GLN343 |
| A | 6Q21003 |
| A | HOH1126 |
| A | HOH1252 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 1011 |
| Chain | Residue |
| A | SER368 |
| A | GLY371 |
| A | PHE372 |
| A | 6Q21003 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 1012 |
| Chain | Residue |
| A | HIS154 |
| A | ASP203 |
| A | PRO205 |
| A | LEU219 |
| site_id | AD4 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 1013 |
| Chain | Residue |
| A | MET273 |
| A | 6Q21003 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 1014 |
| Chain | Residue |
| A | ALA183 |
| A | VAL184 |
| A | HOH1103 |
| B | GLY114 |
| B | ASN115 |
| B | ARG116 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 1015 |
| Chain | Residue |
| A | PRO179 |
| A | ALA180 |
| A | SER295 |
| A | GLY296 |
| A | HIS389 |
| A | PRO390 |
| A | ASP391 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 1016 |
| Chain | Residue |
| A | LEU299 |
| B | ARG335 |
| B | ARG342 |
| B | HOH1113 |
| B | HOH1221 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 1017 |
| Chain | Residue |
| A | GLU366 |
| A | TRP405 |
| A | TYR406 |
| A | THR409 |
| site_id | AD9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 1018 |
| Chain | Residue |
| A | GLU111 |
| A | ARG335 |
| A | HOH1240 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 1019 |
| Chain | Residue |
| A | LYS275 |
| A | HOH1188 |
| site_id | AE2 |
| Number of Residues | 7 |
| Details | binding site for residue ZN B 1001 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | MG1002 |
| B | HOH1150 |
| B | HOH1186 |
| site_id | AE3 |
| Number of Residues | 7 |
| Details | binding site for residue MG B 1002 |
| Chain | Residue |
| B | ASP201 |
| B | ZN1001 |
| B | HOH1147 |
| B | HOH1150 |
| B | HOH1162 |
| B | HOH1178 |
| B | HOH1238 |
| site_id | AE4 |
| Number of Residues | 13 |
| Details | binding site for residue 6Q2 B 1003 |
| Chain | Residue |
| B | TYR159 |
| B | MET273 |
| B | ASP318 |
| B | ASN321 |
| B | TRP332 |
| B | THR333 |
| B | ILE336 |
| B | PHE340 |
| B | GLN369 |
| B | PHE372 |
| B | EDO1012 |
| B | EDO1013 |
| B | HOH1128 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1004 |
| Chain | Residue |
| A | PRO411 |
| B | GLU366 |
| B | TRP405 |
| B | TYR406 |
| B | HOH1127 |
| site_id | AE6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1005 |
| Chain | Residue |
| B | PHE238 |
| B | ARG257 |
| B | ARG261 |
| B | EDO1006 |
| B | HOH1119 |
| B | HOH1196 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1006 |
| Chain | Residue |
| B | ARG257 |
| B | GLN258 |
| B | EDO1005 |
| B | HOH1212 |
| site_id | AE8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1007 |
| Chain | Residue |
| B | LYS262 |
| B | ASP266 |
| B | HOH1102 |
| B | HOH1203 |
| site_id | AE9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 1008 |
| Chain | Residue |
| A | TRP405 |
| B | ASP401 |
| B | ASN402 |
| site_id | AF1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 1009 |
| Chain | Residue |
| B | MET277 |
| B | LYS284 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1010 |
| Chain | Residue |
| A | ASP151 |
| A | HIS152 |
| B | GLY371 |
| B | ASP374 |
| B | TYR375 |
| B | HOH1138 |
| site_id | AF3 |
| Number of Residues | 9 |
| Details | binding site for residue EDO B 1011 |
| Chain | Residue |
| B | HIS160 |
| B | HIS204 |
| B | GLY206 |
| B | VAL207 |
| B | GLU339 |
| B | PHE340 |
| B | GLN343 |
| B | HOH1124 |
| B | HOH1143 |
| site_id | AF4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1012 |
| Chain | Residue |
| B | SER368 |
| B | GLY371 |
| B | PHE372 |
| B | 6Q21003 |
| site_id | AF5 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 1013 |
| Chain | Residue |
| B | MET273 |
| B | 6Q21003 |
| site_id | AF6 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 1014 |
| Chain | Residue |
| B | LYS239 |
| site_id | AF7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1015 |
| Chain | Residue |
| B | HIS154 |
| B | ASP203 |
| B | PRO205 |
| B | LEU219 |
| site_id | AF8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1016 |
| Chain | Residue |
| B | THR293 |
| B | SER294 |
| B | VAL297 |
| B | HOH1303 |
| site_id | AF9 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 1018 |
| Chain | Residue |
| A | VAL297 |
| A | LEU299 |
| B | HOH1142 |
| site_id | AG1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1019 |
| Chain | Residue |
| B | ALA183 |
| B | PHE185 |
| B | ILE190 |
| B | HOH1116 |
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 | 2 |
| 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 | 6 |
| 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 | 2 |
| 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 | 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":"1XOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
