Receptor
PDB id Resolution Class Description Source Keywords
2Q8C 2.05 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF JMJD2A IN TERNARY COMPLEX WITH AN HISTO PEPTIDE AND 2-OXOGLUTARATE HOMO SAPIENS HISTONE DEMETHYLASE HYDROXYLASE JUMONJI 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
AKG A:503;
B:504;
Valid;
Valid;
none;
none;
submit data
146.098 C5 H6 O5 C(CC(...
NI A:501;
B:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
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
2Q8C 2.05 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF JMJD2A IN TERNARY COMPLEX WITH AN HISTO PEPTIDE AND 2-OXOGLUTARATE HOMO SAPIENS HISTONE DEMETHYLASE HYDROXYLASE JUMONJI OXIDOREDUCTASE
Ref.: SPECIFICITY AND MECHANISM OF JMJD2A, A TRIMETHYLLYSINE-SPECIFIC HISTONE DEMETHYLASE. NAT.STRUCT.MOL.BIOL. V. 14 689 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 2Q8C - 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 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: AKG; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 OOG 0.5 0.947368
3 69O 0.458333 0.714286
4 2IT 0.423077 0.615385
5 SHF 0.416667 0.666667
6 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Q8C; Ligand: AKG; Similar sites found: 109
This union binding pocket(no: 1) in the query (biounit: 2q8c.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DRY AAG 0.00486 0.44814 1.23457
2 1DRY AKG 0.00486 0.44814 1.23457
3 4JKV 1KS 0.03042 0.4042 1.42045
4 5UQD AKG 0.000007155 0.55732 1.70455
5 2WBP ZZU 0.008045 0.43219 1.70455
6 2WBP SIN 0.008045 0.43219 1.70455
7 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.004015 0.44058 1.76991
8 2JIG PD2 0.0002083 0.49277 1.78571
9 1NX4 AKG 0.008378 0.40544 1.8315
10 3ZDS HMQ 0.0001105 0.51086 1.98864
11 3ZDS HQ9 0.0001673 0.49141 1.98864
12 3ZDS OMD 0.0003166 0.48416 1.98864
13 3ZDS M8O 0.0004097 0.47799 1.98864
14 1QW9 KHP 0.01517 0.40547 1.98864
15 5KOD AMP 0.0219 0.40131 1.98864
16 1H2K OGA 0.000003786 0.5661 2.00573
17 1H2M OGA 0.000003939 0.5651 2.00573
18 3P3N AKG 0.000005072 0.56002 2.00573
19 4B7E OGA 0.000005535 0.54392 2.00573
20 2WA4 069 0.000003166 0.50323 2.00573
21 3PUR 2HG 0.00006831 0.51074 2.27273
22 4YRD 3IT 0.0007112 0.43064 2.27273
23 2X06 NAD 0.01232 0.42486 2.32558
24 3TYZ PAB 0.01748 0.41557 2.5
25 3TYZ XHP 0.01548 0.41557 2.5
26 4N14 WR7 0.006737 0.41442 2.54777
27 4QNW FMN 0.01856 0.41367 2.55682
28 3W21 AKG 0.006897 0.40003 2.5641
29 1J3R 6PG 0.01405 0.4065 2.63158
30 3KV5 OGA 0.0001547 0.4892 2.84091
31 4BG1 IVL 0.01041 0.42721 2.84091
32 4H3Q ANP 0.01583 0.42062 2.84091
33 5MBC FMN 0.01366 0.41263 2.84091
34 2PYW ADP 0.01814 0.41232 2.84091
35 1C3V NDP 0.04601 0.4013 2.85714
36 1RZM PEP 0.0107 0.40682 2.95858
37 1OIK C26 0.008032 0.4204 2.99003
38 1OIK AKG 0.003501 0.4204 2.99003
39 4R5Z SIN 0.03839 0.40137 3.125
40 5IQT AKG 0.0163 0.4095 3.1746
41 5IQT 6CU 0.02416 0.40501 3.1746
42 5EPA AKG 0.001281 0.44783 3.22581
43 5HES 032 0.02859 0.40325 3.25733
44 3QP8 HL0 0.004015 0.44086 3.26087
45 1G63 FMN 0.02661 0.40599 3.31492
46 5LUN OGA 0.004649 0.42419 3.40909
47 5LUN ARG 0.01683 0.41774 3.40909
48 5WZN A2G 0.007664 0.41433 3.40909
49 2RDQ AKG 0.0001951 0.51616 3.47222
50 5C5T AKG 0.001587 0.45018 3.50877
51 4MNS 2AX 0.01328 0.44647 3.77358
52 1UNB PN1 0.0005967 0.50035 3.85852
53 1UNB AKG 0.0005252 0.50035 3.85852
54 1ODM ASV 0.0007651 0.48851 3.92749
55 4J25 OGA 0.001068 0.45117 3.93013
56 4WUJ FMN 0.02314 0.40541 4.08163
57 3H7J PPY 0.003773 0.4383 4.11523
58 5HV0 AKG 0.00001827 0.55695 4.14747
59 5VSM MET 0.02118 0.40769 4.40252
60 4QXB OGA 0.00001138 0.55355 4.41176
61 4C5N ACP 0.04362 0.40262 4.71014
62 4C5N PXL 0.0455 0.40262 4.71014
63 5JNN 6LM 0.02513 0.40957 4.73684
64 4ZXA H8N 0.0007429 0.46569 4.7619
65 4M26 ZZU 0.01154 0.42897 4.82955
66 4M26 SIN 0.01154 0.42897 4.82955
67 3MPB FRU 0.00836 0.41682 4.87805
68 2YG2 S1P 0.02622 0.4057 5.23256
69 4IAW LIZ 0.01227 0.40636 5.31915
70 2FCU AKG 0.006252 0.41094 5.43131
71 3GC8 B45 0.0334 0.40088 5.68182
72 4U98 ACP 0.02369 0.40066 5.68182
73 3L2B B4P 0.04425 0.40636 5.71429
74 3E2M E2M 0.02118 0.41162 5.94595
75 1GP6 SIN 0.009731 0.43098 5.96591
76 1GP6 DH2 0.009731 0.43098 5.96591
77 1GP6 QUE 0.01035 0.43098 5.96591
78 4MLO PAM 0.006261 0.42786 6.52174
79 3B8X G4M 0.0173 0.42727 6.53409
80 4QM9 CYS 0.005702 0.41284 6.93642
81 4K38 SAM 0.02588 0.4003 7.10227
82 5L9V OGA 0.009751 0.41216 7.14286
83 5I8T LAC 0.01252 0.40122 7.26257
84 1QY1 PRZ 0.02097 0.40809 7.47126
85 2C49 ADN 0.01661 0.4093 7.94702
86 5I0U DCY 0.00007213 0.52182 8
87 5TFZ 7BC 0.0006003 0.47095 8
88 4GJY OGA 0.0000004179 0.61602 8.51064
89 2GC0 PAN 0.01531 0.41279 8.51064
90 4Y3O OGA 0.0001671 0.48644 8.80682
91 4CCO OGA 0.0002434 0.48636 8.80682
92 5HCY 60D 0.02285 0.42595 8.80682
93 5HZX 2GE 0.01474 0.40165 9.09091
94 1OS7 AKG 0.00306 0.4479 9.54064
95 1OS7 TAU 0.00306 0.4479 9.54064
96 4XAC AKG 0.001172 0.4452 9.92064
97 4CCN OGA 0.0003436 0.47 12.2159
98 4CCK OGA 0.0001712 0.48556 12.5
99 1LRH NLA 0.001285 0.45735 13.4969
100 1WBI BTN 0.009499 0.4134 13.9535
101 3E85 BSU 0.01114 0.44272 18.9873
102 1X0P FAD 0.01713 0.40273 26.5734
103 2Y0I AKG 0.000004152 0.57049 28.5714
104 2XUM OGA 0.000004814 0.56306 30
105 4IGQ OGA 0.00000000007633 0.72902 42.3295
106 4IGQ THR M3L GLN 0.00000001857 0.72902 42.3295
107 3PUA OGA 0.0004323 0.46899 46.6667
108 4XCB HY0 0.03345 0.40105 46.6667
109 5IVE 6E8 0.00000000971 0.7707 47.8788
Pocket No.: 2; Query (leader) PDB : 2Q8C; Ligand: AKG; Similar sites found: 17
This union binding pocket(no: 2) in the query (biounit: 2q8c.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1W0O DAN 0.003852 0.43859 1.98864
2 3EWC MCF 0.02562 0.40238 2.27273
3 4Q0L V14 0.03346 0.40204 2.28137
4 4NAO AKG 0.007948 0.40773 2.45399
5 5V1B 8UY 0.005447 0.42392 2.91667
6 2PP3 LGT 0.01465 0.40968 3.40909
7 5ENQ 5QE 0.03235 0.40063 4.54545
8 4M26 AKG 0.01196 0.40087 4.82955
9 3DLS ADP 0.01984 0.4033 5.67164
10 1KHZ ADV 0.03862 0.40385 6.69856
11 5L9B AKG 0.01357 0.40056 7.14286
12 4XT2 43L 0.01138 0.42309 7.69231
13 4JZR 4JR 0.01291 0.40777 8.33333
14 2RG0 CTT 0.03636 0.40561 9.09091
15 2IYG FMN 0.01306 0.41089 9.67742
16 1GQG DCD 0.02885 0.40055 46.6667
17 4XCB AKG 0.009664 0.40046 46.6667
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