Receptor
PDB id Resolution Class Description Source Keywords
2P5B 1.99 Å EC: 1.14.11.- THE COMPLEX STRUCTURE OF JMJD2A AND TRIMETHYLATED H3K36 PEPT HOMO SAPIENS JMJD2A JMJC DOMAIN HISTONE DEMETHYLASE METAL BINDING PROT
Ref.: STRUCTURAL BASIS OF THE RECOGNITION OF A METHYLATED TAIL BY JMJD2A. PROC.NATL.ACAD.SCI.USA V. 104 10818 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:352;
B:352;
Part of Protein;
Part of Protein;
none;
none;
submit data
55.845 Fe [Fe+3...
OGA A:401;
B:402;
Valid;
Valid;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
OXY A:501;
A:502;
B:503;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
31.999 O2 O=O
ZN A:351;
B:351;
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
2P5B 1.99 Å EC: 1.14.11.- THE COMPLEX STRUCTURE OF JMJD2A AND TRIMETHYLATED H3K36 PEPT HOMO SAPIENS JMJD2A JMJC DOMAIN HISTONE DEMETHYLASE METAL BINDING PROT
Ref.: STRUCTURAL BASIS OF THE RECOGNITION OF A METHYLATED TAIL BY JMJD2A. PROC.NATL.ACAD.SCI.USA V. 104 10818 2007
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 2PXJ - OGA C4 H5 N O5 C(C(=O)O)N....
2 2P5B - OGA C4 H5 N O5 C(C(=O)O)N....
3 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
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 2P5B - OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2YBS - S2G C5 H8 O5 C(CC(=O)O)....
2 2P5B - 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 : 2P5B; Ligand: OGA; Similar sites found: 47
This union binding pocket(no: 1) in the query (biounit: 2p5b.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5UQD AKG 0.00001661 0.55793 1.70455
2 2JIG PD2 0.001626 0.44607 1.78571
3 2G30 ALA ALA PHE 0.0334 0.40539 1.93798
4 3ZDS HMQ 0.0004888 0.4525 1.98864
5 3ZDS HQ9 0.0002708 0.43874 1.98864
6 3ZDS OMD 0.0009548 0.43331 1.98864
7 3ZDS M8O 0.001163 0.42976 1.98864
8 4YRD 3IT 0.0007279 0.46557 2.27273
9 3W21 AKG 0.01537 0.40259 2.5641
10 3KV5 OGA 0.0001561 0.50508 2.84091
11 3KV4 OGA 0.0006972 0.47193 2.84091
12 4LJ3 C2E 0.01945 0.40064 2.86738
13 4LOO SB4 0.01217 0.40186 3.125
14 5LUN OGA 0.01593 0.40254 3.40909
15 1ODM ASV 0.00311 0.44068 3.92749
16 4J25 OGA 0.003513 0.43708 3.93013
17 4HIA FMN 0.02182 0.41074 3.97727
18 5HV0 AKG 0.0005083 0.46149 4.14747
19 1ZB6 DIN 0.008206 0.42464 4.23453
20 2CBO TH2 0.01842 0.40622 4.34783
21 2HK9 SKM 0.02185 0.40173 4.72727
22 4ZXA H8N 0.0031 0.43255 4.7619
23 4QM9 CYS 0.005474 0.42686 6.93642
24 5FLJ QUE 0.01603 0.40315 6.98925
25 4K55 H6P 0.004239 0.45036 7.25806
26 5I0U DCY 0.0003317 0.46021 8
27 5TFZ 7BC 0.003906 0.4277 8
28 4GJY OGA 0.000001478 0.61091 8.51064
29 4Y3O OGA 0.0005673 0.47513 8.80682
30 5HES 032 0.009859 0.4133 9.09091
31 5HZX 2GE 0.01106 0.40152 9.09091
32 1QKQ MAN 0.001277 0.4243 10.5634
33 4CCK OGA 0.0005801 0.41832 12.5
34 1LRH NLA 0.004793 0.41864 13.4969
35 5EPA AKG 0.006318 0.42254 18.1818
36 5FUI APY 0.003416 0.45899 22.7273
37 5C5T AKG 0.005833 0.41928 22.7273
38 1OIJ AKG 0.008534 0.41151 27.2727
39 2XUM OGA 0.00001218 0.47776 30
40 3PUA OGA 0.0008661 0.46754 36.3636
41 4XAC AKG 0.003208 0.43806 40.9091
42 4IGQ THR M3L GLN 0.00000001507 0.68151 42.3295
43 4IGQ OGA 0.000000000344 0.58009 42.3295
44 3PUR 2HG 0.0001708 0.50351 45.4545
45 3N9O OGA 0.0003246 0.48733 45.4545
46 3N9P OGA 0.0003877 0.42416 45.4545
47 5IVE 6E8 0.0000002357 0.46195 47.8788
Pocket No.: 2; Query (leader) PDB : 2P5B; Ligand: OGA; Similar sites found: 6
This union binding pocket(no: 2) in the query (biounit: 2p5b.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3G5D 1N1 0.04129 0.41416 2.44755
2 4XV1 904 0.02324 0.41085 3.08219
3 1ZB6 GST 0.008074 0.43054 4.23453
4 2HK5 1BM 0.01361 0.40717 6.66667
5 3NZ1 3NY 0.01977 0.4 7.66284
6 3TW1 AHN 0.01586 0.40351 8.01688
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