Receptor
PDB id Resolution Class Description Source Keywords
6AVS 2.02 Å EC: 1.14.11.27 COMPLEX STRUCTURE OF JMJD5 AND SYMMETRIC MONOMETHYL-ARGININE HOMO SAPIENS DEMETHYLASE JUMONJI HISTONE ENDOPEPTIDASE EXOPEPTIDASE OXIDOREDUCTASE
Ref.: SPECIFIC RECOGNITION OF ARGININE METHYLATED HISTONE JMJD5 AND JMJD7. SCI REP V. 8 3275 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NMM A:502;
Valid;
none;
submit data
188.228 C7 H16 N4 O2 [H]/N...
ZN A:501;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6F4T 1.22 Å EC: 1.14.11.27 HUMAN JMJD5 (W414C) IN COMPLEX WITH MN(II), NOG AND RCCD1 (1 (COMPLEX-5) HOMO SAPIENS OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATE DIOXYGENASEJMJC DOMAIN LYSINE-SPECIFIC DEMETHYLASE 8 JMJC DOMAIN-CONPROTEIN 5 ARGINYL C-3 HYDROXYLASE JMJD5 KDM8 OXYGENASEDNA-BINDING METAL-BINDING TRANSLATION DSBH FACIAL TRIADCYTOPLASM JMJC HYDROXYLASE JMJC DEMETHYLASE KDMS POST- TRANSLATIONAL MODIFICATIONS PTM BETA-HYDROXYLATION HYDROARGININE HYDROXYLATION RCC1 DOMAIN-CONTAINING PROTEIN 1 RREGULATOR OF CHROMOSOME CONDENSATION 40S RIBOSOMAL PROTEINRPS6 RIBOSOME BIOGENESIS TRANSCRIPTION EPIGENETIC REGULASIGNALING DEVELOPMENT CELL STRUCTURE TRANSCRIPTION ACTIVATOR/INHIBITOR PHOSPHORYLATION CANCER POLYMORPHISM
Ref.: JMJD5 IS A HUMAN ARGINYL C-3 HYDROXYLASE. NAT COMMUN V. 9 1180 2018
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
4 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
5 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
6 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
7 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
8 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
4 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
5 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
6 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
7 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
8 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
4 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
5 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
6 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
7 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
8 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NMM; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 NMM 1 1
2 HAR 0.707317 0.744186
3 1KJ 0.681818 0.790698
4 ILO 0.658537 0.837838
5 RPI 0.630435 0.615385
6 2KJ 0.625 0.733333
7 D20 0.625 0.790698
8 DA2 0.6 0.833333
9 CIR 0.6 0.725
10 AS1 0.591837 0.761905
11 4JK 0.590909 0.75
12 VUR 0.590909 0.769231
13 2MR 0.586957 0.972222
14 3KJ 0.586957 0.76087
15 ARG 0.585366 0.888889
16 DAR 0.585366 0.888889
17 WT2 0.577778 0.763158
18 JM2 0.574468 0.780488
19 LN6 0.55102 0.731707
20 JM7 0.54 0.738095
21 3AR 0.531915 0.846154
22 VIO 0.520833 0.731707
23 HRG 0.511111 0.888889
24 JM6 0.509434 0.785714
25 JM8 0.509434 0.761905
26 JM4 0.509434 0.744186
27 JM5 0.5 0.761905
28 2YH 0.489796 0.619048
29 ALY 0.478261 0.642857
30 MLZ 0.477273 0.74359
31 NNH 0.466667 0.688889
32 ORN 0.414634 0.714286
33 MLY 0.413043 0.636364
34 I58 0.411765 0.731707
35 AHL 0.408163 0.612245
36 5KJ 0.403846 0.68
37 AAR 0.4 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6F4T; Ligand: OGA; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 6f4t.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2XUM OGA 46.2745
2 3P3N AKG 46.2745
3 2Y0I AKG 46.2745
4 4B7E OGA 46.2745
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