Receptor
PDB id Resolution Class Description Source Keywords
2YBP 2.02 Å EC: 1.14.11.27 JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36 PEPTIDE (30-41) HOMO SAPIENS OXIDOREDUCTASE-PEPTIDE COMPLEX NON-HEME IRON DIOXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FACIAL TRIAD METAL BINDIPROTEIN EPIGENETIC AND TRANSCRIPTION REGULATION CHROMATINREGULATOR HYDROXYLATION
Ref.: THE ONCOMETABOLITE 2-HYDROXYGLUTARATE INHIBITS HISTONE LYSINE DEMETHYLASES. EMBO REP. V. 12 463 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2HG A:1359;
B:1358;
Valid;
Valid;
none;
none;
submit data
148.114 C5 H8 O5 C(CC(...
GOL A:1358;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NI A:1356;
B:1356;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
ZN A:1357;
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
2YBP 2.02 Å EC: 1.14.11.27 JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36 PEPTIDE (30-41) HOMO SAPIENS OXIDOREDUCTASE-PEPTIDE COMPLEX NON-HEME IRON DIOXYGENASE DOUBLE-STRANDED BETA HELIX DSBH FACIAL TRIAD METAL BINDIPROTEIN EPIGENETIC AND TRANSCRIPTION REGULATION CHROMATINREGULATOR HYDROXYLATION
Ref.: THE ONCOMETABOLITE 2-HYDROXYGLUTARATE INHIBITS HISTONE LYSINE DEMETHYLASES. EMBO REP. V. 12 463 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 2YBP - 2HG C5 H8 O5 C(CC(=O)O)....
2 2YBS - S2G C5 H8 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 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: 2HG; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 S2G 1 1
2 2HG 1 1
3 LMR 0.461538 0.809524
4 DMR 0.461538 0.809524
5 MLT 0.461538 0.809524
6 2RH 0.444444 0.652174
7 DGY 0.44 0.666667
8 DGL 0.433333 0.653846
9 GGL 0.433333 0.653846
10 GLU 0.433333 0.653846
11 HOC 0.411765 0.62963
12 HCT 0.40625 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YBP; Ligand: 2HG; Similar sites found: 131
This union binding pocket(no: 1) in the query (biounit: 2ybp.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DRY AAG 0.01657 0.42112 1.23457
2 1DRY AKG 0.01657 0.42112 1.23457
3 3S7O LBV 0.006263 0.44879 1.45773
4 4F4P 0SB 0.03855 0.42705 1.4652
5 1VJY 460 0.008699 0.44236 1.65016
6 4MOB ADP 0.01322 0.40015 1.80723
7 1ODM ASV 0.001264 0.47831 1.81269
8 3ZDS HMQ 0.000301 0.48835 1.83727
9 3ZDS HQ9 0.0004002 0.47237 1.83727
10 3ZDS OMD 0.0007898 0.46426 1.83727
11 5LRT ADP 0.002606 0.46237 1.83727
12 3ZDS M8O 0.0009739 0.4596 1.83727
13 3T1A 5MA 0.01164 0.4177 1.83727
14 2XIQ MLC 0.03203 0.40751 1.83727
15 2G30 ALA ALA PHE 0.0185 0.41971 1.93798
16 1H2K OGA 0.00001332 0.54221 2.00573
17 1H2M OGA 0.00001409 0.54145 2.00573
18 3P3N AKG 0.00001739 0.5374 2.00573
19 4B7E OGA 0.00003277 0.52483 2.00573
20 2WA4 069 0.00001725 0.49227 2.00573
21 4BXF AKG 0.00105 0.45023 2.09974
22 2I7N ACO 0.02395 0.40671 2.22222
23 4YRD 3IT 0.0006311 0.46581 2.22841
24 4QMN DB8 0.009784 0.44493 2.25806
25 2V77 PAY 0.013 0.41308 2.26537
26 5F7V GLC GLC GLC GLC 0.01721 0.41483 2.3622
27 3B2Q ATP 0.03408 0.40227 2.3622
28 3G5D 1N1 0.01784 0.44385 2.44755
29 3TYZ XHP 0.02066 0.41193 2.5
30 3KV5 OGA 0.0001779 0.48971 2.62467
31 3KV4 OGA 0.0007333 0.45865 2.62467
32 3PUA OGA 0.0009154 0.45448 2.62467
33 4B0T ADP 0.007414 0.43958 2.62467
34 4USF 6UI 0.00655 0.43999 2.63158
35 4H3Q ANP 0.02529 0.40791 2.76243
36 5BVE 4VG 0.01603 0.45021 2.77008
37 5VFC 9BA 0.04273 0.40326 2.89389
38 4TWP AXI 0.02563 0.42764 2.95203
39 1OIK AKG 0.004955 0.41778 2.99003
40 5WZN A2G 0.006922 0.41783 3.14961
41 3WYJ H78 0.03721 0.43169 3.16206
42 4BKJ STI 0.008693 0.43619 3.1746
43 5EPA AKG 0.003376 0.4296 3.22581
44 5HES 032 0.008291 0.43204 3.25733
45 3QP8 HL0 0.005898 0.43159 3.26087
46 4CSV STI 0.009784 0.43052 3.27273
47 5LUN ARG 0.01096 0.43109 3.40909
48 5LUN OGA 0.004547 0.42401 3.40909
49 4P7X YCP 0.00614 0.43247 3.42466
50 4P7X AKG 0.00614 0.43247 3.42466
51 4QM9 CYS 0.01137 0.40137 3.46821
52 5C5T AKG 0.001936 0.42081 3.50877
53 5UR1 YY9 0.03942 0.40633 3.53698
54 4P5Z Q7M 0.02734 0.41958 3.60111
55 4DSU BZI 0.006196 0.40637 3.7037
56 2WQP WQP 0.0114 0.43167 3.72493
57 4XV1 904 0.01107 0.43893 3.76712
58 5JGA 6KC 0.04563 0.40258 3.80952
59 4J25 OGA 0.001956 0.4393 3.93013
60 4ASE AV9 0.02805 0.41042 3.96601
61 2OFV 242 0.006658 0.45335 3.97112
62 4HIA FMN 0.004939 0.46078 3.97727
63 5HZX 2GE 0.003708 0.43337 3.97727
64 5FIT AP2 0.01291 0.4103 4.08163
65 5DKK FMN 0.0112 0.4223 4.13793
66 5HV0 AKG 0.0000597 0.52982 4.14747
67 1ZB6 DIN 0.005053 0.45112 4.23453
68 5MBC FMN 0.0216 0.4021 4.24929
69 5MF5 C2E 0.03026 0.40575 4.29688
70 2CBO TH2 0.01033 0.40906 4.34783
71 5SVV FMN 0.0249 0.40559 4.37956
72 4NPL AKG 0.004133 0.42359 4.4
73 4M26 SIN 0.02419 0.4122 4.46194
74 2JIG PD2 0.00035 0.48259 4.46429
75 5H2U 1N1 0.01631 0.41164 4.49438
76 5HCY 60D 0.003899 0.47208 4.53172
77 4ZXA H8N 0.0009286 0.43537 4.7619
78 3GZ8 APR 0.02985 0.40162 4.93827
79 2XVD AS6 0.01176 0.43277 4.96689
80 3SXF BK5 0.02398 0.42037 4.98688
81 4J1Q NDP 0.03279 0.40804 4.98688
82 4N1T 2GD 0.0338 0.40995 5.03145
83 5VCV 1N1 0.0152 0.42133 5.14469
84 5KWY C3S 0.01208 0.41573 5.26316
85 4U0I 0LI 0.01714 0.42601 5.39683
86 2FCU AKG 0.0121 0.40061 5.43131
87 3AVS OGA 0.0000000002194 0.79405 5.77428
88 5FP3 3JI 0.00000002863 0.72104 5.77428
89 5UQD AKG 0.00001031 0.53236 5.77428
90 1GP6 DH2 0.00738 0.43842 5.89888
91 1GP6 SIN 0.00738 0.43842 5.89888
92 1GP6 QUE 0.009482 0.43426 5.89888
93 4RFR RHN 0.001399 0.46566 5.91133
94 2WEI VGG 0.02081 0.40092 6.27178
95 4UF0 MMK 0.00006467 0.52722 6.29921
96 5UIU 8CG 0.009998 0.4365 6.50155
97 4MLO PAM 0.01059 0.41526 6.52174
98 2HK5 1BM 0.005181 0.4411 6.66667
99 4K38 SAM 0.02188 0.40569 6.75676
100 3EWK FAD 0.02213 0.40608 7.04846
101 1W0O DAN 0.01665 0.40376 7.34908
102 4OCT AKG 0.0007892 0.42949 7.65766
103 5I0U DCY 0.0002384 0.49382 8
104 5TFZ 7BC 0.00138 0.45265 8
105 4Y3O OGA 0.0003274 0.47551 8.13648
106 5MJA 7O3 0.008293 0.42256 8.85246
107 1NCQ W11 0.01425 0.41507 8.8983
108 1GZW GAL BGC 0.009293 0.43111 8.95522
109 3DOO SKM 0.00856 0.41733 9.38628
110 5FLJ QUE 0.009726 0.42734 9.67742
111 4XAC AKG 0.004689 0.4184 9.92064
112 5DEY 59T 0.01727 0.44459 10.4377
113 2IUW AKG 0.0006608 0.46825 12.605
114 1QKQ MAN 0.000886 0.42029 12.6761
115 2RKV ZBA 0.04272 0.40939 13.1234
116 2RKV COA 0.04279 0.40619 13.1234
117 1LRH NLA 0.002673 0.44096 13.4969
118 5DJT FMN 0.02394 0.40416 16.5517
119 1MDC PLM 0.01968 0.41257 26.5152
120 1X0P FAD 0.01876 0.40275 26.5734
121 2Y0I AKG 0.0000291 0.52797 28.5714
122 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.0108 0.4612 29.5918
123 2XUM OGA 0.00001604 0.53993 30
124 4LIT AKG 0.0007229 0.45919 33.3333
125 4IGQ THR M3L GLN 0.000000006916 0.74372 41.3889
126 4IGQ OGA 0.000000000197 0.67995 41.3889
127 5X2Z 3LM 0.03201 0.4051 41.6667
128 2DQU CPD 0.03686 0.402 41.6667
129 5FWJ MMK 0.00000002606 0.68951 42.2572
130 5A3T MMK 0.0000000009132 0.82064 42.7822
131 5IVE 6E8 0.00000004998 0.72544 47.8788
132 5I8T LAC 0.01127 0.40472 50
Pocket No.: 2; Query (leader) PDB : 2YBP; Ligand: 2HG; Similar sites found: 16
This union binding pocket(no: 2) in the query (biounit: 2ybp.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GQG DCD 0.02902 0.4017 2.28571
2 2GU8 796 0.04482 0.42102 2.37389
3 4LJ3 C2E 0.02705 0.40712 2.86738
4 4PAB THG 0.0216 0.40465 3.67454
5 1ZB6 GST 0.005054 0.45255 4.23453
6 2ZX7 ZX7 0.02484 0.40239 4.72441
7 5H86 BCO 0.03679 0.405 5.95238
8 5L4S NAP 0.04222 0.40934 7.2327
9 5L4S 6KX 0.04222 0.40934 7.2327
10 3VEH 0GA 0.0224 0.40036 7.61155
11 1KGI T4A 0.01653 0.4164 7.87402
12 2QUN FUD 0.02336 0.40013 10
13 5XDT ZI7 0.007759 0.43988 10.4987
14 5XDT MB3 0.04016 0.40835 10.4987
15 2J9D AMP 0.01837 0.4068 11.7647
16 2H8H H8H 0.008966 0.42518 41.6667
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