Receptor
PDB id Resolution Class Description Source Keywords
5FWE 2.05 Å EC: 1.14.11.- JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15) R3ME2S PEPTIDE HOMO SAPIENS JMJD2A OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATE DIOXOXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FACIAL TRIAD DEMETHYLASE HISTONE JMJC DOMAIN METAL BINDING PROTEIN EPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: ARGININE DEMETHYLATION IS CATALYSED BY A SUBSET OF HISTONE LYSINE DEMETHYLASES. NAT.COMMUN. V. 7 11974 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI B:1356;
A:1355;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
CL A:1357;
B:1358;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
GOL B:1360;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
OGA A:1358;
B:1359;
Valid;
Valid;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
ZN A:1356;
B:1357;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FWE 2.05 Å EC: 1.14.11.- JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15) R3ME2S PEPTIDE HOMO SAPIENS JMJD2A OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATE DIOXOXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FACIAL TRIAD DEMETHYLASE HISTONE JMJC DOMAIN METAL BINDING PROTEIN EPIGENETIC AND TRANSCRIPTION REGULATION CHROMATIN REGULATOHYDROXYLATION
Ref.: ARGININE DEMETHYLATION IS CATALYSED BY A SUBSET OF HISTONE LYSINE DEMETHYLASES. NAT.COMMUN. V. 7 11974 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 5FWE - OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 5FWE - OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5FWE - OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: OGA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 OGA 1 1
2 AAC 0.461538 0.827586
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FWE; Ligand: OGA; Similar sites found: 71
This union binding pocket(no: 1) in the query (biounit: 5fwe.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DXI TRE 0.02386 0.40024 1.65563
2 1ODM ASV 0.0006113 0.49399 1.81269
3 3ZDS HMQ 0.0000867 0.51654 1.83727
4 3ZDS HQ9 0.0001318 0.49693 1.83727
5 3ZDS OMD 0.0002714 0.48768 1.83727
6 3ZDS M8O 0.0003208 0.48375 1.83727
7 5KOD AMP 0.02193 0.40119 1.83727
8 1H2M OGA 0.01917 0.41402 2.00573
9 1H2K OGA 0.02045 0.41233 2.00573
10 4B7E OGA 0.02982 0.40592 2.00573
11 4YRD 3IT 0.0008811 0.45283 2.22841
12 3TYZ PAB 0.01739 0.4147 2.5
13 3TYZ XHP 0.01541 0.4147 2.5
14 3W21 AKG 0.007979 0.407 2.5641
15 3KV5 OGA 0.0001157 0.49437 2.62467
16 3KV4 OGA 0.0003075 0.4755 2.62467
17 3PUA OGA 0.0003383 0.47461 2.62467
18 2PYW ADP 0.01593 0.41502 2.62467
19 4H3Q ANP 0.01466 0.42257 2.76243
20 1OIJ AKG 0.004697 0.40664 2.99003
21 5EPA AKG 0.001593 0.44473 3.22581
22 5HES 032 0.02339 0.40823 3.25733
23 1G63 FMN 0.03194 0.4011 3.31492
24 2FHJ MFN 0.01669 0.40985 3.37838
25 5LUN OGA 0.004555 0.40272 3.40909
26 4QM9 CYS 0.005065 0.41652 3.46821
27 2RDQ AKG 0.0002649 0.5087 3.47222
28 5C5T AKG 0.00169 0.41318 3.50877
29 4J25 OGA 0.0008773 0.44278 3.93013
30 5HV0 AKG 0.00002913 0.54493 4.14747
31 5MBC FMN 0.01499 0.41038 4.24929
32 4QXB OGA 0.00001057 0.50527 4.41176
33 4M26 SIN 0.01552 0.42154 4.46194
34 4M26 ZZU 0.01552 0.42154 4.46194
35 2JIG PD2 0.0002541 0.44763 4.46429
36 5HCY 60D 0.01918 0.43013 4.53172
37 3BXO UPP 0.01621 0.40755 4.60251
38 4ZXA H8N 0.0008791 0.42487 4.7619
39 3JRS A8S 0.01874 0.4122 4.80769
40 2YG2 S1P 0.02808 0.40377 5.23256
41 2FCU AKG 0.007501 0.41179 5.43131
42 3DLS ADP 0.01927 0.40471 5.67164
43 3L2B B4P 0.04604 0.40452 5.71429
44 5UQD AKG 0.000008703 0.55288 5.77428
45 1GP6 QUE 0.005887 0.44475 5.89888
46 1GP6 DH2 0.005522 0.44475 5.89888
47 1GP6 SIN 0.005522 0.44475 5.89888
48 3K3K A8S 0.02488 0.40387 6.16114
49 4MLO PAM 0.006765 0.4257 6.52174
50 4XCB AKG 0.01125 0.40117 6.89655
51 5I8T LAC 0.009565 0.4074 7.26257
52 5I0U DCY 0.0000939 0.51537 8
53 5TFZ 7BC 0.0008789 0.42524 8
54 4Y3O OGA 0.0002201 0.47965 8.13648
55 3ACL 3F1 0.01873 0.4015 8.44595
56 4GJY OGA 0.0000003905 0.61907 8.51064
57 4XAC AKG 0.001085 0.44698 9.92064
58 4CCK OGA 0.0002068 0.47974 11.5486
59 1QD1 FON 0.02912 0.40575 12
60 1LRH NLA 0.001034 0.41395 13.4969
61 3PUR 2HG 0.00005698 0.49742 16.5354
62 3N9O OGA 0.0002807 0.47414 16.5354
63 3N9Q OGA 0.0002899 0.47344 16.5354
64 3N9P OGA 0.0003063 0.47156 16.5354
65 2Y0I AKG 0.02373 0.41151 28.5714
66 2XUM OGA 0.02304 0.40927 30
67 3E85 BSU 0.01278 0.43895 33.3333
68 5WZN A2G 0.006615 0.4178 33.3333
69 4IGQ OGA 0.00000000005872 0.73432 41.3889
70 4IGQ THR M3L GLN 0.00000001504 0.73432 41.3889
71 5IVE 6E8 0.00000001326 0.76293 47.8788
Pocket No.: 2; Query (leader) PDB : 5FWE; Ligand: OGA; Similar sites found: 3
This union binding pocket(no: 2) in the query (biounit: 5fwe.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IJP 1EH 0.02784 0.40057 4.46927
2 5JNN 6LM 0.02555 0.40854 4.73684
3 3KDJ A8S 0.01123 0.42038 5.37975
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