Receptor
PDB id Resolution Class Description Source Keywords
6AX3 2.25 Å EC: 1.14.11.27 COMPLEX STRUCTURE OF JMJD5 AND SYMMETRIC DIMETHYL-ARGININE ( HOMO SAPIENS DEMETHYLASE JUMONJI HISTONE ENDOPEPTIDASE EXOPEPTIDASE
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
2MR A:501;
Valid;
none;
submit data
202.254 C8 H18 N4 O2 CN/C(...
AKG A:502;
Invalid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
ZN A:503;
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: 2MR; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 2MR 1 1
2 NMM 0.586957 0.972222
3 CIR 0.55814 0.707317
4 DAR 0.545455 0.864865
5 ARG 0.545455 0.864865
6 ILO 0.543478 0.815789
7 WT2 0.510204 0.74359
8 3AR 0.5 0.825
9 DA2 0.5 0.857143
10 VIO 0.490196 0.714286
11 3KJ 0.490196 0.744681
12 HAR 0.489796 0.727273
13 4JK 0.489796 0.731707
14 VUR 0.489796 0.75
15 1KJ 0.480769 0.772727
16 JM2 0.480769 0.761905
17 MLZ 0.478261 0.725
18 D20 0.472727 0.772727
19 LN6 0.462963 0.714286
20 2YH 0.461538 0.604651
21 JM8 0.45614 0.744186
22 JM7 0.454545 0.72093
23 ALY 0.44898 0.627907
24 2KJ 0.446429 0.717391
25 RPI 0.444444 0.603774
26 JM6 0.431034 0.767442
27 JM4 0.431034 0.767442
28 JM5 0.423729 0.744186
29 AS1 0.421053 0.744186
30 HRG 0.42 0.864865
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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