5F37
Crystal structure of human KDM4A in complex with compound 58
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | HIS188 |
| A | GLU190 |
| A | HIS276 |
| A | N5J403 |
| A | HOH504 |
| A | HOH524 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 402 |
| Chain | Residue |
| A | CYS308 |
| A | CYS234 |
| A | HIS240 |
| A | CYS306 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | binding site for residue N5J A 403 |
| Chain | Residue |
| A | TYR132 |
| A | TYR177 |
| A | PHE185 |
| A | HIS188 |
| A | ASN198 |
| A | LYS206 |
| A | TRP208 |
| A | LYS241 |
| A | HIS276 |
| A | ZN401 |
| A | HOH504 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | GLY170 |
| A | GLU190 |
| A | SER288 |
| A | THR289 |
| A | ASN290 |
| A | HOH524 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | THR83 |
| A | SER230 |
| A | HIS240 |
| A | MET242 |
| A | THR243 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | LEU65 |
| A | GLY138 |
| A | THR139 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | ILE150 |
| A | GLY151 |
| A | LEU153 |
| A | ASN290 |
| A | HOH506 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 408 |
| Chain | Residue |
| A | ASN9 |
| A | PRO10 |
| A | SER11 |
| A | ALA12 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 409 |
| Chain | Residue |
| A | SER11 |
| A | ALA12 |
| A | ARG13 |
| A | PRO212 |
| A | PHE257 |
| A | ASP258 |
| A | HOH546 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 410 |
| Chain | Residue |
| A | ALA134 |
| A | ASP135 |
| A | LYS241 |
| A | HOH503 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 411 |
| Chain | Residue |
| A | PRO50 |
| A | LYS51 |
| A | TRP53 |
| A | TYR199 |
| A | EDO415 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 412 |
| Chain | Residue |
| A | GLU235 |
| A | ALA236 |
| A | PHE237 |
| A | LEU238 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 413 |
| Chain | Residue |
| A | LYS251 |
| A | GLY254 |
| A | ILE255 |
| A | PHE257 |
| A | EDO414 |
| site_id | AD5 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 414 |
| Chain | Residue |
| A | PHE257 |
| A | EDO413 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 415 |
| Chain | Residue |
| A | HIS201 |
| A | EDO411 |
| site_id | AD7 |
| Number of Residues | 3 |
| Details | binding site for residue DMS A 416 |
| Chain | Residue |
| A | TYR59 |
| A | ARG98 |
| A | PHE202 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue DMS A 417 |
| Chain | Residue |
| A | LYS54 |
| A | PRO55 |
| A | ARG56 |
| A | ALA57 |
| A | GLU142 |
| A | HIS144 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 401 |
| Chain | Residue |
| B | HIS188 |
| B | GLU190 |
| B | HIS276 |
| B | N5J403 |
| B | HOH540 |
| B | HOH545 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 402 |
| Chain | Residue |
| B | CYS234 |
| B | HIS240 |
| B | CYS306 |
| B | CYS308 |
| site_id | AE2 |
| Number of Residues | 11 |
| Details | binding site for residue N5J B 403 |
| Chain | Residue |
| B | LYS241 |
| B | HIS276 |
| B | ZN401 |
| B | HOH545 |
| B | TYR132 |
| B | TYR177 |
| B | PHE185 |
| B | HIS188 |
| B | ASN198 |
| B | LYS206 |
| B | TRP208 |
| site_id | AE3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 404 |
| Chain | Residue |
| B | GLY170 |
| B | GLU190 |
| B | SER288 |
| B | THR289 |
| B | HOH540 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| B | ASN9 |
| B | PRO10 |
| B | SER11 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | PRO10 |
| B | ALA12 |
| B | GLU214 |
| B | HIS215 |
| site_id | AE6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | SER11 |
| B | ALA12 |
| B | ARG13 |
| B | PRO212 |
| B | PHE257 |
| B | ASP258 |
| B | HOH578 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 408 |
| Chain | Residue |
| B | PRO256 |
| B | PHE257 |
| B | EDO417 |
| site_id | AE8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 409 |
| Chain | Residue |
| B | LEU65 |
| B | GLY138 |
| B | THR139 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 410 |
| Chain | Residue |
| B | THR83 |
| B | PHE227 |
| B | SER230 |
| B | HIS240 |
| B | THR243 |
| site_id | AF1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 411 |
| Chain | Residue |
| B | ILE150 |
| B | GLY151 |
| B | ARG152 |
| B | LEU153 |
| B | ASN290 |
| B | HOH520 |
| site_id | AF2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 412 |
| Chain | Residue |
| B | LEU8 |
| B | ASN9 |
| B | GLN37 |
| site_id | AF3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 413 |
| Chain | Residue |
| B | GLU23 |
| B | ARG29 |
| B | HOH583 |
| site_id | AF4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 414 |
| Chain | Residue |
| B | ASN86 |
| B | ALA134 |
| B | ASP135 |
| B | SER184 |
| B | LYS241 |
| B | HOH507 |
| B | HOH628 |
| site_id | AF5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 415 |
| Chain | Residue |
| B | HIS188 |
| B | THR189 |
| B | ASP191 |
| B | ARG239 |
| B | HOH598 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 416 |
| Chain | Residue |
| B | LYS224 |
| B | GLU235 |
| B | ALA236 |
| B | PHE237 |
| B | LEU238 |
| B | HOH591 |
| site_id | AF7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 417 |
| Chain | Residue |
| B | LYS251 |
| B | GLY254 |
| B | ILE255 |
| B | PRO256 |
| B | EDO408 |
| site_id | AF8 |
| Number of Residues | 1 |
| Details | binding site for residue DMS B 418 |
| Chain | Residue |
| B | GLN88 |
| site_id | AF9 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 401 |
| Chain | Residue |
| C | HIS188 |
| C | GLU190 |
| C | HIS276 |
| C | N5J403 |
| C | HOH536 |
| C | HOH561 |
| site_id | AG1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 402 |
| Chain | Residue |
| C | CYS234 |
| C | HIS240 |
| C | CYS306 |
| C | CYS308 |
| site_id | AG2 |
| Number of Residues | 11 |
| Details | binding site for residue N5J C 403 |
| Chain | Residue |
| C | TYR132 |
| C | TYR177 |
| C | PHE185 |
| C | HIS188 |
| C | LYS206 |
| C | LYS241 |
| C | HIS276 |
| C | ZN401 |
| C | EDO410 |
| C | HOH536 |
| C | HOH561 |
| site_id | AG3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 404 |
| Chain | Residue |
| C | GLY170 |
| C | TYR177 |
| C | GLU190 |
| C | SER288 |
| C | THR289 |
| C | HOH536 |
| site_id | AG4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 405 |
| Chain | Residue |
| C | THR83 |
| C | PHE227 |
| C | THR243 |
| site_id | AG5 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 406 |
| Chain | Residue |
| C | GLY138 |
| C | THR139 |
| site_id | AG6 |
| Number of Residues | 8 |
| Details | binding site for residue EDO C 407 |
| Chain | Residue |
| C | SER11 |
| C | ALA12 |
| C | ARG13 |
| C | PRO212 |
| C | PHE257 |
| C | ASP258 |
| C | HOH531 |
| C | HOH556 |
| site_id | AG7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 408 |
| Chain | Residue |
| C | GLU23 |
| C | TYR30 |
| C | HOH527 |
| site_id | AG8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 409 |
| Chain | Residue |
| C | ILE150 |
| C | GLY151 |
| C | ARG152 |
| C | LEU153 |
| C | ASN290 |
| C | HOH511 |
| site_id | AG9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 410 |
| Chain | Residue |
| C | ALA134 |
| C | ASP135 |
| C | LYS241 |
| C | N5J403 |
| C | HOH515 |
| site_id | AH1 |
| Number of Residues | 3 |
| Details | binding site for residue DMS C 411 |
| Chain | Residue |
| C | TYR59 |
| C | ILE62 |
| C | ARG98 |
| site_id | AH2 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 401 |
| Chain | Residue |
| D | HIS188 |
| D | GLU190 |
| D | HIS276 |
| D | N5J403 |
| D | HOH528 |
| D | HOH530 |
| site_id | AH3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 402 |
| Chain | Residue |
| D | CYS234 |
| D | HIS240 |
| D | CYS306 |
| D | CYS308 |
| site_id | AH4 |
| Number of Residues | 12 |
| Details | binding site for residue N5J D 403 |
| Chain | Residue |
| D | TYR132 |
| D | TYR177 |
| D | PHE185 |
| D | HIS188 |
| D | ASN198 |
| D | LYS206 |
| D | TRP208 |
| D | LYS241 |
| D | HIS276 |
| D | ZN401 |
| D | HOH528 |
| D | HOH530 |
| site_id | AH5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 404 |
| Chain | Residue |
| D | LYS224 |
| D | GLU235 |
| D | ALA236 |
| D | PHE237 |
| D | LEU238 |
| D | HOH519 |
| D | HOH601 |
| site_id | AH6 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 405 |
| Chain | Residue |
| D | HIS201 |
| site_id | AH7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 406 |
| Chain | Residue |
| D | THR83 |
| D | PHE227 |
| D | SER230 |
| D | PHE237 |
| D | THR243 |
| D | HOH598 |
| site_id | AH8 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 407 |
| Chain | Residue |
| D | SER11 |
| D | ALA12 |
| D | ARG13 |
| D | PRO212 |
| D | PHE257 |
| D | ASP258 |
| D | HOH564 |
| site_id | AH9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 408 |
| Chain | Residue |
| D | SER11 |
| D | GLU214 |
| D | HIS215 |
| D | HOH623 |
| site_id | AI1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 409 |
| Chain | Residue |
| D | LYS251 |
| D | GLY254 |
| D | ILE255 |
| D | EDO411 |
| site_id | AI2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 410 |
| Chain | Residue |
| A | GLU161 |
| A | LYS162 |
| D | ARG56 |
| D | ASP61 |
| site_id | AI3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO D 411 |
| Chain | Residue |
| D | PHE257 |
| D | EDO409 |
| site_id | AI4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 412 |
| Chain | Residue |
| D | GLU23 |
| D | ARG29 |
| D | PHE353 |
| D | HOH520 |
| site_id | AI5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 413 |
| Chain | Residue |
| D | ALA134 |
| D | ASP135 |
| D | SER184 |
| D | LYS241 |
| D | HOH545 |
| D | HOH560 |
| site_id | AI6 |
| Number of Residues | 2 |
| Details | binding site for residue DMS D 414 |
| Chain | Residue |
| D | TYR59 |
| D | ARG98 |
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 | 664 |
| 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 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"N-acetylalanine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]} |
| 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 |
