Receptor
PDB id Resolution Class Description Source Keywords
2Q8E 2.05 Å EC: 1.14.11.- SPECIFICITY AND MECHANISM OF JMJD2A, A TRIMETHYLLYSINE- SPECIFIC HISTONE DEMETHYLASE HOMO SAPIENS HISTONE DEMETHYLASE HYDROXYLASE N-OXALYLGLYCINE OXIDOREDUCTASE
Ref.: SPECIFICITY AND MECHANISM OF JMJD2A, A TRIMETHYLLYSINE-SPECIFIC HISTONE DEMETHYLASE. NAT.STRUCT.MOL.BIOL. V. 14 689 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI A:501;
B:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
OGA A:503;
B:504;
Valid;
Valid;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
ZN A:505;
B:506;
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
2Q8E 2.05 Å EC: 1.14.11.- SPECIFICITY AND MECHANISM OF JMJD2A, A TRIMETHYLLYSINE- SPECIFIC HISTONE DEMETHYLASE HOMO SAPIENS HISTONE DEMETHYLASE HYDROXYLASE N-OXALYLGLYCINE OXIDOREDUCTASE
Ref.: SPECIFICITY AND MECHANISM OF JMJD2A, A TRIMETHYLLYSINE-SPECIFIC HISTONE DEMETHYLASE. NAT.STRUCT.MOL.BIOL. V. 14 689 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 2Q8E - OGA C4 H5 N O5 C(C(=O)O)N....
2 2Q8D - SIN C4 H6 O4 O=C([O-])C....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 2Q8C - AKG C5 H6 O5 C(CC(=O)O)....
2 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
3 2OS2 - OGA C4 H5 N O5 C(C(=O)O)N....
4 2Q8E - OGA C4 H5 N O5 C(C(=O)O)N....
5 2Q8D - SIN C4 H6 O4 O=C([O-])C....
6 2PXJ - OGA C4 H5 N O5 C(C(=O)O)N....
7 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 2Q8C - AKG C5 H6 O5 C(CC(=O)O)....
2 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
3 2OS2 - OGA C4 H5 N O5 C(C(=O)O)N....
4 2Q8E - OGA C4 H5 N O5 C(C(=O)O)N....
5 2Q8D - SIN C4 H6 O4 O=C([O-])C....
6 2PXJ - OGA C4 H5 N O5 C(C(=O)O)N....
7 5A7W - 35M C19 H14 N2 O5 c1cc(ccc1C....
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 : 2Q8E; Ligand: OGA; Similar sites found: 111
This union binding pocket(no: 1) in the query (biounit: 2q8e.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DRY AAG 0.01158 0.42931 1.23457
2 1DRY AKG 0.01158 0.42931 1.23457
3 4F4P 0SB 0.043 0.4243 1.4652
4 1VJY 460 0.007377 0.44632 1.65016
5 5UQD AKG 0.00001077 0.55277 1.70455
6 2JIG PD2 0.0003027 0.48527 1.78571
7 2G30 ALA ALA PHE 0.004356 0.40896 1.93798
8 4XDA ADP 0.04922 0.40407 1.94175
9 3ZDS HMQ 0.0002673 0.49087 1.98864
10 3ZDS HQ9 0.0003919 0.47274 1.98864
11 3ZDS OMD 0.0007652 0.46484 1.98864
12 3ZDS M8O 0.0009347 0.4364 1.98864
13 3T1A 5MA 0.01413 0.41288 1.98864
14 1H2K OGA 0.000007297 0.55624 2.00573
15 1H2M OGA 0.00000795 0.55418 2.00573
16 3P3N AKG 0.000008879 0.55171 2.00573
17 4B7E OGA 0.00001838 0.53759 2.00573
18 2WA4 069 0.00001009 0.50095 2.00573
19 3PUR 2HG 0.00008741 0.50504 2.27273
20 3N9O OGA 0.0002809 0.46475 2.27273
21 3N9P OGA 0.000325 0.46175 2.27273
22 5LRT ADP 0.003339 0.45668 2.27273
23 4YRD 3IT 0.0009013 0.45394 2.27273
24 1GQG DCD 0.03091 0.40004 2.28571
25 4NAO AKG 0.01047 0.40672 2.45399
26 5N87 N66 0.01023 0.44196 2.55591
27 5F7V GLC GLC GLC GLC 0.01115 0.4249 2.55682
28 4TWP AXI 0.0261 0.42668 2.58303
29 5XDT MB3 0.04111 0.40796 2.5974
30 4USF 6UI 0.009229 0.41742 2.63158
31 1J3R 6PG 0.01661 0.40198 2.63158
32 3KV5 OGA 0.0001208 0.4984 2.84091
33 3KV4 OGA 0.000439 0.46956 2.84091
34 3PUA OGA 0.000693 0.46048 2.84091
35 5BVE 4VG 0.01352 0.45477 2.84091
36 4B0T ADP 0.006579 0.4425 2.84091
37 5MBC FMN 0.015 0.41063 2.84091
38 4LJ3 C2E 0.02726 0.40698 2.86738
39 5DQ8 FLF 0.03482 0.40203 2.91667
40 4XV1 904 0.01395 0.43298 3.08219
41 1OUK 084 0.02294 0.45656 3.125
42 4BKJ STI 0.008339 0.43713 3.1746
43 5EPA AKG 0.002721 0.43427 3.22581
44 5HES 032 0.007906 0.43315 3.25733
45 3QP8 HL0 0.004516 0.44012 3.26087
46 2XMY CDK 0.02895 0.43716 3.3557
47 5LUN OGA 0.004499 0.42468 3.40909
48 5LUN ARG 0.009239 0.41284 3.40909
49 5WZN A2G 0.009262 0.41136 3.40909
50 2WQP WQP 0.0123 0.42969 3.4384
51 5UR1 YY9 0.03546 0.40856 3.53698
52 4P5Z Q7M 0.03346 0.41434 3.69318
53 4J25 OGA 0.001686 0.44163 3.93013
54 2OFV 242 0.005354 0.45878 3.97112
55 4PAB THG 0.01446 0.41207 3.97727
56 5DKK FMN 0.01202 0.42061 4.13793
57 5HV0 AKG 0.00004617 0.53523 4.14747
58 5MF5 C2E 0.0278 0.40787 4.29688
59 2HK9 SKM 0.007495 0.41568 4.72727
60 4ZXA H8N 0.0007284 0.43958 4.7619
61 4M26 SIN 0.01985 0.41669 4.82955
62 3GZ8 APR 0.02546 0.40545 4.93827
63 4N1T 2GD 0.02863 0.41426 5.03145
64 5KWY C3S 0.01103 0.41789 5.26316
65 4J1Q NDP 0.02042 0.41971 5.39773
66 2FCU AKG 0.008853 0.40748 5.43131
67 1GP6 SIN 0.007647 0.43758 5.96591
68 1GP6 DH2 0.007647 0.43758 5.96591
69 1GP6 QUE 0.008155 0.43758 5.96591
70 4MLO PAM 0.01242 0.41224 6.52174
71 3SAO DBH 0.006967 0.43091 6.875
72 4QM9 CYS 0.005661 0.41624 6.93642
73 5FLJ QUE 0.00974 0.42675 6.98925
74 3EWK FAD 0.02727 0.40098 7.04846
75 4K55 H6P 0.002741 0.44972 7.25806
76 1QY1 PRZ 0.02641 0.40393 7.47126
77 2WZ5 MET 0.002184 0.4378 7.84314
78 1KGI T4A 0.02891 0.4029 7.87402
79 3KDN CAP 0.04832 0.4165 7.95455
80 5I0U DCY 0.000127 0.50783 8
81 5TFZ 7BC 0.000891 0.43594 8
82 4GJY OGA 0.0000005412 0.61644 8.51064
83 4Y3O OGA 0.0002597 0.48041 8.80682
84 5HCY 60D 0.004862 0.46647 8.80682
85 4CCO OGA 0.000581 0.45452 8.80682
86 5MJA 7O3 0.008306 0.42246 8.85246
87 1NCQ W11 0.01283 0.41747 8.8983
88 5HZX 2GE 0.003706 0.40318 9.09091
89 5JKG 6LF 0.04045 0.41076 9.32476
90 3DOO SKM 0.007177 0.42112 9.38628
91 4XAC AKG 0.002864 0.42907 9.92064
92 5DEY 59T 0.01304 0.45202 10.4377
93 1QKQ MAN 0.0004421 0.45104 10.5634
94 2J9D AMP 0.01419 0.41266 10.9244
95 4CCN OGA 0.0004235 0.46935 12.2159
96 4CCK OGA 0.0002361 0.4687 12.5
97 1LRH NLA 0.001301 0.45678 13.4969
98 5C5T AKG 0.002418 0.41752 25
99 1MDC PLM 0.01967 0.41276 26.5152
100 1X0P FAD 0.01782 0.40391 26.5734
101 2Y0I AKG 0.00001766 0.53807 28.5714
102 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.00918 0.46559 29.5918
103 2XUM OGA 0.000008317 0.55494 30
104 3WYJ H78 0.03655 0.43226 31.25
105 5X2Z 3LM 0.03239 0.40478 31.25
106 2DQU CPD 0.03309 0.40448 31.25
107 1OIK AKG 0.004033 0.42103 37.5
108 5I8T LAC 0.01397 0.4 37.5
109 4IGQ THR M3L GLN 0.000000003135 0.76215 42.3295
110 4IGQ OGA 0.00000000007802 0.69633 42.3295
111 5IVE 6E8 0.00000004269 0.72936 47.8788
Pocket No.: 2; Query (leader) PDB : 2Q8E; Ligand: OGA; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 2q8e.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PS9 FMN 0.03253 0.40221 1.70455
2 2GU8 796 0.04094 0.42348 2.37389
3 3G5D 1N1 0.01781 0.44347 2.44755
4 5UIU 8CG 0.01034 0.43562 2.78638
5 5W4W 9WG 0.03493 0.40633 3.69318
6 2CBO TH2 0.01447 0.40164 4.34783
7 4K38 SAM 0.0189 0.40849 7.10227
8 5IXJ THR 0.0397 0.405 7.38636
9 1GZW GAL BGC 0.01397 0.41894 8.95522
10 4N14 WR7 0.006079 0.42174 31.25
Feedback