5VGI
Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue NI A 501 |
| Chain | Residue |
| A | HIS188 |
| A | GLU190 |
| A | HIS276 |
| A | 9DJ503 |
| A | HOH609 |
| A | HOH620 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 502 |
| Chain | Residue |
| A | CYS308 |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| site_id | AC3 |
| Number of Residues | 17 |
| Details | binding site for residue 9DJ A 503 |
| Chain | Residue |
| A | GLN73 |
| A | ASN86 |
| A | TYR132 |
| A | SER184 |
| A | PHE185 |
| A | HIS188 |
| A | ASN198 |
| A | LYS206 |
| A | TRP208 |
| A | HIS240 |
| A | LYS241 |
| A | HIS276 |
| A | ARG309 |
| A | NI501 |
| A | HOH609 |
| A | HOH620 |
| A | HOH631 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue NI B 501 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | 9DJ503 |
| B | HOH606 |
| B | HOH642 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 502 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AC6 |
| Number of Residues | 12 |
| Details | binding site for residue 9DJ B 503 |
| Chain | Residue |
| B | ASN86 |
| B | TYR132 |
| B | PHE185 |
| B | HIS188 |
| B | ASN198 |
| B | LYS206 |
| B | HIS240 |
| B | LYS241 |
| B | HIS276 |
| B | ARG309 |
| B | NI501 |
| B | HOH642 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue NI C 501 |
| Chain | Residue |
| C | HIS188 |
| C | GLU190 |
| C | HIS276 |
| C | 9DJ503 |
| C | HOH617 |
| C | HOH619 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 502 |
| Chain | Residue |
| C | CYS234 |
| C | HIS240 |
| C | CYS306 |
| C | CYS308 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | binding site for residue 9DJ C 503 |
| Chain | Residue |
| C | GLN73 |
| C | ASN86 |
| C | TYR132 |
| C | ASP135 |
| C | PHE185 |
| C | HIS188 |
| C | LYS206 |
| C | HIS240 |
| C | HIS276 |
| C | ARG309 |
| C | NI501 |
| C | HOH617 |
| C | HOH619 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue NI D 501 |
| Chain | Residue |
| D | HIS188 |
| D | GLU190 |
| D | HIS276 |
| D | 9DJ503 |
| D | HOH614 |
| D | HOH634 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 502 |
| Chain | Residue |
| D | CYS234 |
| D | HIS240 |
| D | CYS306 |
| D | CYS308 |
| site_id | AD3 |
| Number of Residues | 17 |
| Details | binding site for residue 9DJ D 503 |
| Chain | Residue |
| D | ASN86 |
| D | TYR132 |
| D | PHE185 |
| D | HIS188 |
| D | ASN198 |
| D | LYS206 |
| D | TRP208 |
| D | ARG239 |
| D | HIS240 |
| D | LYS241 |
| D | HIS276 |
| D | ARG309 |
| D | MET312 |
| D | NI501 |
| D | HOH614 |
| D | HOH634 |
| D | HOH641 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 168 |
| Details | Domain: {"description":"JmjN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00537","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 498 |
| Details | Domain: {"description":"JmjC","evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00538","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16677698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26741168","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 16 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"5F2W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F32","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F37","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F39","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F3G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5F5I","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"B2RXH2","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
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 |
