Receptor
PDB id Resolution Class Description Source Keywords
4QXB 1.6 Å EC: 1.14.11.27 CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE KDM2A-H3K36ME3 WITH MUS MUSCULUS CUPIN SUBFAMILY FE(II)/2-OG DIOXYGENASE JMJC DOMAIN HISTONDEMETHYLASE OXIDOREDUCTASE-STRUCTURAL PROTEIN COMPLEX
Ref.: A MOLECULAR THREADING MECHANISM UNDERLIES JUMONJI L DEMETHYLASE KDM2A REGULATION OF METHYLATED H3K36. GENES DEV. V. 28 1758 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI C:601;
A:601;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
OGA C:600;
A:600;
Valid;
Valid;
none;
none;
submit data
147.086 C4 H5 N O5 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4QXB 1.6 Å EC: 1.14.11.27 CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE KDM2A-H3K36ME3 WITH MUS MUSCULUS CUPIN SUBFAMILY FE(II)/2-OG DIOXYGENASE JMJC DOMAIN HISTONDEMETHYLASE OXIDOREDUCTASE-STRUCTURAL PROTEIN COMPLEX
Ref.: A MOLECULAR THREADING MECHANISM UNDERLIES JUMONJI L DEMETHYLASE KDM2A REGULATION OF METHYLATED H3K36. GENES DEV. V. 28 1758 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 4QX7 - AKG C5 H6 O5 C(CC(=O)O)....
2 4QXB - OGA C4 H5 N O5 C(C(=O)O)N....
3 4QX8 - AKG C5 H6 O5 C(CC(=O)O)....
4 4TN7 - SIN C4 H6 O4 O=C([O-])C....
5 4QXC - OGA C4 H5 N O5 C(C(=O)O)N....
6 4QXH - OGA C4 H5 N O5 C(C(=O)O)N....
7 4QWN - AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 4QX7 - AKG C5 H6 O5 C(CC(=O)O)....
2 4QXB - OGA C4 H5 N O5 C(C(=O)O)N....
3 4QX8 - AKG C5 H6 O5 C(CC(=O)O)....
4 4TN7 - SIN C4 H6 O4 O=C([O-])C....
5 4QXC - OGA C4 H5 N O5 C(C(=O)O)N....
6 4QXH - OGA C4 H5 N O5 C(C(=O)O)N....
7 4QWN - AKG C5 H6 O5 C(CC(=O)O)....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4QX7 - AKG C5 H6 O5 C(CC(=O)O)....
2 4QXB - OGA C4 H5 N O5 C(C(=O)O)N....
3 4QX8 - AKG C5 H6 O5 C(CC(=O)O)....
4 4TN7 - SIN C4 H6 O4 O=C([O-])C....
5 4QXC - OGA C4 H5 N O5 C(C(=O)O)N....
6 4QXH - OGA C4 H5 N O5 C(C(=O)O)N....
7 4QWN - AKG C5 H6 O5 C(CC(=O)O)....
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 : 4QXB; Ligand: OGA; Similar sites found: 128
This union binding pocket(no: 1) in the query (biounit: 4qxb.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VRV YSD 0.04624 0.41143 1.84502
2 3T03 3T0 0.01692 0.40108 2.11268
3 4UF0 MMK 0.001049 0.45525 2.12766
4 4MLO PAM 0.003031 0.43543 2.53623
5 4OSP 2V4 0.01342 0.40144 2.6616
6 4BQY FNT 0.00003009 0.44968 2.77778
7 3HQR OGA 0.0004022 0.449 2.84553
8 5V1B 8UY 0.0001294 0.49999 2.91667
9 2V0U FMN 0.0004959 0.40825 3.42466
10 4JZR 4JR 0.0008946 0.45292 4.16667
11 5L9V OGA 0.0001356 0.47962 4.36508
12 5L9B AKG 0.0001598 0.47681 4.36508
13 4MNS 2AX 0.03225 0.42006 4.40252
14 5LY2 OGA 0.000008079 0.56171 4.41176
15 2Q8C AKG 0.00001138 0.55355 4.41176
16 3AVS OGA 0.0000221 0.52925 4.41176
17 5FWE OGA 0.00001057 0.50527 4.41176
18 5DQ8 FLF 0.02222 0.40545 4.41176
19 1A78 TDG 0.00751 0.42249 4.47761
20 5KWY C3S 0.004139 0.43109 4.51128
21 1WHT BZS 0.01403 0.40007 4.57516
22 4RFR RHN 0.00112 0.46333 4.92611
23 5IXH OTP 0.02829 0.41907 4.96894
24 5C5T AKG 0.00139 0.44383 5.26316
25 4D42 W0I 0.04088 0.41659 5.31915
26 4D42 NAP 0.04088 0.41659 5.31915
27 3W21 AKG 0.00004566 0.52758 5.49451
28 3MPB FRU 0.002726 0.4043 5.69106
29 1C1L GAL BGC 0.01719 0.40166 5.83942
30 5IXG OTP 0.02449 0.42501 5.88235
31 1G42 CP2 0.01232 0.40356 5.88235
32 4WN5 MVC 0.007571 0.42756 6.08696
33 5DKK FMN 0.0002986 0.41873 6.2069
34 4D06 NAR 0.01828 0.40663 6.36042
35 3QRC SCR 0.001231 0.42745 6.36943
36 4IAW LIZ 0.00878 0.40574 6.38298
37 5L7G 6QE 0.02015 0.40609 6.55738
38 1NX4 AKG 0.0008741 0.4632 6.59341
39 5KR7 6X9 0.000007986 0.52393 7.29483
40 5FWJ MMK 0.0006399 0.45983 7.35294
41 4WVW SLT 0.002659 0.42545 7.35294
42 4P7X YCP 0.000947 0.41982 7.35294
43 4P7X AKG 0.000947 0.41982 7.35294
44 4YRD 3IT 0.006654 0.40923 7.35294
45 1LRH NLA 0.0005786 0.45313 7.36196
46 5H9P TD2 0.001974 0.43125 7.59494
47 1ULE GLA GAL NAG 0.007277 0.41859 8
48 4IGQ OGA 0.00002926 0.52515 8.82353
49 2FCU AKG 0.0003171 0.48387 8.82353
50 5FP3 3JI 0.00004431 0.43384 8.82353
51 4ZXA H8N 0.003817 0.42297 8.82353
52 1GP6 DH2 0.01377 0.41753 8.82353
53 1GP6 SIN 0.01377 0.41753 8.82353
54 1GP6 QUE 0.0147 0.41753 8.82353
55 4BLW AMP 0.008205 0.41615 8.82353
56 4MZU TYD 0.01078 0.40855 8.82353
57 4Q0L V14 0.02775 0.40334 8.82353
58 4W9N TCL 0.01573 0.40111 8.82353
59 5FLJ QUE 0.02273 0.40344 9.13978
60 4J25 OGA 0.0008437 0.46379 9.17031
61 4OMJ 2TX 0.01273 0.42847 9.35252
62 1J3R 6PG 0.006217 0.40468 9.47368
63 5GLT BGC GAL NAG GAL 0.0006338 0.40623 9.50704
64 2P7Q GG6 0.003257 0.42625 9.77444
65 3ZXE PGZ 0.009278 0.40038 9.77444
66 2GJ5 VD3 0.03104 0.41228 9.87654
67 3VV1 GAL FUC 0.005441 0.43047 10
68 4Y3O OGA 0.003706 0.42974 10.2941
69 1WBI BTN 0.003453 0.40048 10.2941
70 4QM9 CYS 0.0005352 0.47898 10.4046
71 5HV0 AKG 0.0005367 0.47195 11.5207
72 5EFW FMN 0.0002549 0.42022 11.7241
73 5DJU FMN 0.0004915 0.40413 11.7241
74 4XCB HY0 0.000204 0.51219 11.7647
75 4XCB AKG 0.00004109 0.50762 11.7647
76 2OG7 SIN 0.001297 0.45337 11.7647
77 2JIG PD2 0.002507 0.43166 11.7647
78 5N87 N66 0.02742 0.41312 11.7647
79 5BV6 35G 0.01606 0.406 11.8421
80 5OO5 UUA 0.00191 0.40367 12.0968
81 2YMZ LAT 0.004395 0.41906 13.0769
82 2IUW AKG 0.0002204 0.48182 13.2353
83 4M26 AKG 0.0008782 0.46351 13.2353
84 4M26 SIN 0.005063 0.44118 13.2353
85 1QY1 PRZ 0.01278 0.41445 13.2353
86 4EES FMN 0.0005981 0.40289 13.913
87 5I0U DCY 0.00009526 0.5024 14
88 4NAO AKG 0.00006551 0.52239 14.1104
89 5A3T MMK 0.000633 0.49353 14.7059
90 4QYN RTL 0.02569 0.40073 15.7895
91 5UQD AKG 0.0000155 0.5558 16.1765
92 1IF7 SBR 0.01705 0.45628 16.1765
93 4GCZ FMN 0.001079 0.40102 16.1765
94 4TW7 37K 0.001544 0.46745 17.1875
95 5TFZ 7BC 0.008316 0.40687 17.3333
96 3P3N AKG 0.000005476 0.57188 17.6471
97 1H2M OGA 0.000005545 0.57076 17.6471
98 1H2K OGA 0.000006827 0.56631 17.6471
99 2Y0I AKG 0.00001906 0.54429 17.6471
100 5IVE 6E8 0.0001295 0.52915 17.6471
101 2WA4 069 0.000008587 0.52237 17.6471
102 4E1O PLP PVH 0.01976 0.40652 17.6471
103 1TIW TFB 0.03047 0.41463 19.1176
104 4O8A FAD 0.037 0.40298 19.1176
105 3EW2 BTN 0.007961 0.40777 20
106 5U98 1KX 0.02641 0.4189 22.2222
107 5DJT FMN 0.0004787 0.48157 22.9508
108 5M0T AKG 0.001001 0.45936 23.5294
109 5LUN OGA 0.001986 0.44207 23.5294
110 5KF6 FAD 0.03037 0.40515 23.5294
111 4WW7 AMP 0.02438 0.40031 25
112 2PR5 FMN 0.0007236 0.40679 25.7576
113 4BXF AKG 0.0004147 0.4774 26.6667
114 4LIT AKG 0.005455 0.42228 26.6667
115 5JSP DQY 0.002397 0.41663 29.4118
116 2A1X AKG 0.0004796 0.48066 33.3333
117 2ET1 GLV 0.00638 0.41914 33.3333
118 5MY8 RXZ 0.02777 0.40194 33.3333
119 5EPA AKG 0.000003006 0.56005 33.8235
120 4OCT AKG 0.0001677 0.47559 35.2941
121 4NPL AKG 0.0013 0.45538 35.2941
122 1OIJ AKG 0.0008093 0.46798 40
123 1OIK AKG 0.001432 0.45753 40
124 2WKQ FMN 0.0004432 0.41304 40
125 4B7E OGA 0.000009615 0.55965 41.1765
126 2XUM OGA 0.000004309 0.57704 45
127 4XAC AKG 0.000002044 0.55073 46.6667
128 3H7J PPY 0.003707 0.40542 46.6667
Pocket No.: 2; Query (leader) PDB : 4QXB; Ligand: OGA; Similar sites found: 3
This union binding pocket(no: 2) in the query (biounit: 4qxb.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5ML3 DL3 0.01848 0.4286 4.41176
2 1QKQ MAN 0.01389 0.43497 4.92958
3 5EQU AKG 0.02302 0.40057 8.82353
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