6H4U
Crystal structure of human KDM4A in complex with compound 34b
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | HIS188 |
| A | GLU190 |
| A | HIS276 |
| A | FO2403 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 402 |
| Chain | Residue |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| A | CYS308 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | binding site for residue FO2 A 403 |
| Chain | Residue |
| A | ASP135 |
| A | TYR177 |
| A | PHE185 |
| A | HIS188 |
| A | GLU190 |
| A | LYS206 |
| A | TRP208 |
| A | HIS276 |
| A | ZN401 |
| A | TYR132 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | binding site for residue DMS A 404 |
| Chain | Residue |
| A | ASN9 |
| A | ARG13 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | binding site for residue GOL A 405 |
| Chain | Residue |
| A | VAL75 |
| A | THR76 |
| A | GLY77 |
| A | THR126 |
| A | PHE127 |
| C | VAL75 |
| C | THR76 |
| C | GLY77 |
| C | THR126 |
| C | HOH521 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | binding site for residue CL A 406 |
| Chain | Residue |
| A | ARG98 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue ZN B 401 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | FO2403 |
| B | HOH512 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 402 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | binding site for residue FO2 B 403 |
| Chain | Residue |
| B | TYR132 |
| B | GLU169 |
| B | TYR175 |
| B | TYR177 |
| B | PHE185 |
| B | HIS188 |
| B | GLU190 |
| B | LYS206 |
| B | TRP208 |
| B | HIS276 |
| B | ZN401 |
| B | HOH512 |
| B | HOH545 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue DMS B 404 |
| Chain | Residue |
| B | TYR111 |
| B | PHE114 |
| B | THR261 |
| B | HIS281 |
| site_id | AD2 |
| Number of Residues | 1 |
| Details | binding site for residue DMS B 405 |
| Chain | Residue |
| B | HOH559 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue ZN C 401 |
| Chain | Residue |
| C | HIS188 |
| C | GLU190 |
| C | HIS276 |
| C | FO2403 |
| C | HOH503 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 402 |
| Chain | Residue |
| C | CYS234 |
| C | HIS240 |
| C | CYS306 |
| C | CYS308 |
| site_id | AD5 |
| Number of Residues | 12 |
| Details | binding site for residue FO2 C 403 |
| Chain | Residue |
| C | TYR132 |
| C | TYR177 |
| C | PHE185 |
| C | HIS188 |
| C | GLU190 |
| C | ASP191 |
| C | LYS206 |
| C | TRP208 |
| C | HIS276 |
| C | ZN401 |
| C | HOH503 |
| C | HOH618 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue DMS C 404 |
| Chain | Residue |
| C | LEU222 |
| C | TYR253 |
| site_id | AD7 |
| Number of Residues | 2 |
| Details | binding site for residue DMS C 405 |
| Chain | Residue |
| C | PHE114 |
| C | HIS281 |
| site_id | AD8 |
| Number of Residues | 1 |
| Details | binding site for residue CL C 406 |
| Chain | Residue |
| C | ARG98 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue ZN D 401 |
| Chain | Residue |
| D | HIS188 |
| D | GLU190 |
| D | HIS276 |
| D | FO2403 |
| D | HOH511 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 402 |
| Chain | Residue |
| D | CYS234 |
| D | HIS240 |
| D | CYS306 |
| D | CYS308 |
| site_id | AE2 |
| Number of Residues | 10 |
| Details | binding site for residue FO2 D 403 |
| Chain | Residue |
| D | TRP208 |
| D | HIS276 |
| D | ZN401 |
| D | HOH511 |
| D | TYR132 |
| D | TYR177 |
| D | PHE185 |
| D | HIS188 |
| D | GLU190 |
| D | LYS206 |
| site_id | AE3 |
| Number of Residues | 9 |
| Details | binding site for residue GOL D 404 |
| Chain | Residue |
| B | VAL75 |
| B | THR76 |
| B | GLY77 |
| B | THR126 |
| D | VAL75 |
| D | THR76 |
| D | GLY77 |
| D | THR126 |
| D | PHE127 |
| site_id | AE4 |
| Number of Residues | 1 |
| Details | binding site for residue CL D 405 |
| Chain | Residue |
| D | ARG98 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16677698 |
| Chain | Residue | Details |
| A | TYR132 | |
| D | TYR132 | |
| D | ASN198 | |
| D | LYS206 | |
| A | ASN198 | |
| A | LYS206 | |
| B | TYR132 | |
| B | ASN198 | |
| B | LYS206 | |
| C | TYR132 | |
| C | ASN198 | |
| C | LYS206 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00538, ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168 |
| Chain | Residue | Details |
| A | HIS188 | |
| A | HIS276 | |
| B | HIS188 | |
| B | HIS276 | |
| C | HIS188 | |
| C | HIS276 | |
| D | HIS188 | |
| D | HIS276 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16677698, ECO:0000305|PubMed:26741168 |
| Chain | Residue | Details |
| A | GLU190 | |
| B | GLU190 | |
| C | GLU190 | |
| D | GLU190 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0007744|PDB:5F2W, ECO:0007744|PDB:5F32, ECO:0007744|PDB:5F37, ECO:0007744|PDB:5F39, ECO:0007744|PDB:5F3E, ECO:0007744|PDB:5F3G, ECO:0007744|PDB:5F5I |
| Chain | Residue | Details |
| A | CYS234 | |
| C | HIS240 | |
| C | CYS306 | |
| C | CYS308 | |
| D | CYS234 | |
| D | HIS240 | |
| D | CYS306 | |
| D | CYS308 | |
| A | HIS240 | |
| A | CYS306 | |
| A | CYS308 | |
| B | CYS234 | |
| B | HIS240 | |
| B | CYS306 | |
| B | CYS308 | |
| C | CYS234 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:B2RXH2 |
| Chain | Residue | Details |
| A | LYS241 | |
| B | LYS241 | |
| C | LYS241 | |
| D | LYS241 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: N-acetylalanine => ECO:0007744|PubMed:19413330 |
| Chain | Residue | Details |
| A | ALA2 | |
| B | ALA2 | |
| C | ALA2 | |
| D | ALA2 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| A | GLY170 | hydrogen bond acceptor, steric role |
| A | TYR177 | hydrogen bond donor, steric role |
| A | HIS188 | metal ligand |
| A | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| A | HIS276 | metal ligand |
| A | SER288 | hydrogen bond donor, steric role |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| B | GLY170 | hydrogen bond acceptor, steric role |
| B | TYR177 | hydrogen bond donor, steric role |
| B | HIS188 | metal ligand |
| B | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| B | HIS276 | metal ligand |
| B | SER288 | hydrogen bond donor, steric role |
| site_id | MCSA3 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| C | GLY170 | hydrogen bond acceptor, steric role |
| C | TYR177 | hydrogen bond donor, steric role |
| C | HIS188 | metal ligand |
| C | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| C | HIS276 | metal ligand |
| C | SER288 | hydrogen bond donor, steric role |
| site_id | MCSA4 |
| Number of Residues | 6 |
| Details | M-CSA 370 |
| Chain | Residue | Details |
| D | GLY170 | hydrogen bond acceptor, steric role |
| D | TYR177 | hydrogen bond donor, steric role |
| D | HIS188 | metal ligand |
| D | GLU190 | attractive charge-charge interaction, hydrogen bond acceptor, metal ligand, steric role |
| D | HIS276 | metal ligand |
| D | SER288 | hydrogen bond donor, steric role |
