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 | 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 |
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 |
