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 (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6I9L - PD2 C7 H5 N O4 c1cnc(cc1C....
4 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
5 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
6 6I9M - 2HG C5 H8 O5 C(CC(=O)O)....
7 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
9 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
10 6I9N - S2G C5 H8 O5 C(CC(=O)O)....
11 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6I9L - PD2 C7 H5 N O4 c1cnc(cc1C....
4 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
5 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
6 6I9M - 2HG C5 H8 O5 C(CC(=O)O)....
7 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
9 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
10 6I9N - S2G C5 H8 O5 C(CC(=O)O)....
11 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6I9L - PD2 C7 H5 N O4 c1cnc(cc1C....
4 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
5 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
6 6I9M - 2HG C5 H8 O5 C(CC(=O)O)....
7 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
9 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
10 6I9N - S2G C5 H8 O5 C(CC(=O)O)....
11 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands (2D)
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 DA2 0.5 0.857143
9 3AR 0.5 0.825
10 VIO 0.490196 0.714286
11 3KJ 0.490196 0.744681
12 4JK 0.489796 0.731707
13 VUR 0.489796 0.75
14 HAR 0.489796 0.727273
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 JM4 0.431034 0.767442
27 JM6 0.431034 0.767442
28 JM5 0.423729 0.744186
29 AS1 0.421053 0.744186
30 HRG 0.42 0.864865
Similar Ligands (3D)
Ligand no: 1; Ligand: 2MR; Similar ligands found: 69
No: Ligand Similarity coefficient
1 MLY 0.9077
2 NPI 0.9065
3 J9Y 0.9044
4 XRS 0.9043
5 SB7 0.8976
6 XI7 0.8967
7 GGB 0.8967
8 GNW 0.8950
9 6FG 0.8936
10 AX4 0.8927
11 DA3 0.8927
12 11X 0.8905
13 OA1 0.8901
14 NRG 0.8890
15 EGV 0.8883
16 SB9 0.8874
17 1PS 0.8866
18 848 0.8862
19 MMS 0.8862
20 AX5 0.8835
21 V15 0.8826
22 4KJ 0.8825
23 D4G 0.8824
24 TZM 0.8819
25 M3L 0.8816
26 TZP 0.8806
27 LPA 0.8805
28 IYR 0.8794
29 26P 0.8786
30 54F 0.8783
31 3IP 0.8782
32 M5P 0.8782
33 DAH 0.8774
34 6C5 0.8766
35 6C9 0.8759
36 3VW 0.8758
37 94X 0.8737
38 KYN 0.8737
39 C53 0.8731
40 SOJ 0.8724
41 EQW 0.8723
42 1YO 0.8708
43 SZ7 0.8703
44 6HO 0.8701
45 3GC 0.8692
46 BZQ 0.8686
47 IAR 0.8677
48 JGB 0.8675
49 IJ1 0.8657
50 JKK 0.8657
51 5TO 0.8656
52 HPZ 0.8649
53 6C8 0.8644
54 DHH 0.8642
55 M2E 0.8638
56 0V7 0.8634
57 L06 0.8629
58 TYR 0.8626
59 D53 0.8623
60 M5E 0.8609
61 C82 0.8607
62 1BN 0.8576
63 ENO 0.8570
64 XOG 0.8568
65 PFF 0.8567
66 PHQ DAL 0.8564
67 2B4 0.8540
68 KF5 0.8531
69 2NP 0.8524
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: 5
This union binding pocket(no: 1) in the query (biounit: 6f4t.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 6GDY AKG 39.6078
2 2XUM OGA 46.2745
3 3P3N AKG 46.2745
4 2Y0I AKG 46.2745
5 4B7E OGA 46.2745
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