Receptor
PDB id Resolution Class Description Source Keywords
5FP3 2.05 Å EC: 1.14.11.- CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND JARID1 (KDM5) FAMILIES OF HISTONE LYSINE DEMETHYLASES HOMO SAPIENS OXIDOREDUCTASE INHIBITOR JMJD3 KDM6B JUMONJI
Ref.: CELL PENETRANT INHIBITORS OF THE KDM4 AND KDM5 FAMI HISTONE LYSINE DEMETHYLASES. 1. 3-AMINO-4-PYRIDINE CARBOXYLATE DERIVATIVES. J.MED.CHEM. V. 59 1357 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BCN B:2640;
A:2640;
B:2641;
A:2641;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
163.172 C6 H13 N O4 C(CO)...
3JI B:1;
A:1;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.045;
Atoms found LESS than expected: % Diff = 0.045;
ic50 = 1.259 uM
301.317 C16 H17 N2 O4 c1ccc...
MG B:2639;
A:2642;
B:2642;
A:2639;
Part of Protein;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
CO A:3000;
B:3000;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.933 Co [Co+2...
ZN A:2000;
B:2000;
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
5FP3 2.05 Å EC: 1.14.11.- CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND JARID1 (KDM5) FAMILIES OF HISTONE LYSINE DEMETHYLASES HOMO SAPIENS OXIDOREDUCTASE INHIBITOR JMJD3 KDM6B JUMONJI
Ref.: CELL PENETRANT INHIBITORS OF THE KDM4 AND KDM5 FAMI HISTONE LYSINE DEMETHYLASES. 1. 3-AMINO-4-PYRIDINE CARBOXYLATE DERIVATIVES. J.MED.CHEM. V. 59 1357 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 4ASK - K0I C22 H23 N5 O2 c1ccc2c(c1....
2 5FP3 ic50 = 1.259 uM 3JI C16 H17 N2 O4 c1ccc(cc1)....
3 4EYU - OGA C4 H5 N O5 C(C(=O)O)N....
4 2XUE - AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4ASK - K0I C22 H23 N5 O2 c1ccc2c(c1....
2 5FP3 ic50 = 1.259 uM 3JI C16 H17 N2 O4 c1ccc(cc1)....
3 4EYU - OGA C4 H5 N O5 C(C(=O)O)N....
4 2XUE - AKG C5 H6 O5 C(CC(=O)O)....
5 3AVS - OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4ASK - K0I C22 H23 N5 O2 c1ccc2c(c1....
2 5FP3 ic50 = 1.259 uM 3JI C16 H17 N2 O4 c1ccc(cc1)....
3 4EYU - OGA C4 H5 N O5 C(C(=O)O)N....
4 2XUE - AKG C5 H6 O5 C(CC(=O)O)....
5 3AVS - OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3JI; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 3JI 1 1
2 YC8 0.528571 0.754386
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FP3; Ligand: 3JI; Similar sites found: 65
This union binding pocket(no: 1) in the query (biounit: 5fp3.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3B00 16A 0.008849 0.41972 1.47059
2 5C3R HMU 0.0002005 0.47788 1.74927
3 5C3R AKG 0.0002005 0.47788 1.74927
4 2RDQ AKG 0.0001233 0.46316 2.08333
5 4J25 OGA 0.0002873 0.50812 2.18341
6 3KV5 OGA 0.0008027 0.47875 2.2541
7 3Q8G PEE 0.02403 0.4025 2.7451
8 4YRD 3IT 0.0001616 0.51619 2.78552
9 3PUR 2HG 0.001524 0.46957 2.94118
10 1ODM ASV 0.0009559 0.43527 3.02115
11 4QJP V1F 0.004879 0.40582 3.04183
12 1UPR 4IP 0.009309 0.42632 3.25203
13 4FFG 0U8 0.01881 0.4067 3.45528
14 4WVW SLT 0.009247 0.42232 3.47222
15 1DRY AAG 0.006747 0.40293 3.7037
16 1DRY AKG 0.006747 0.40293 3.7037
17 4GJY OGA 0.000007273 0.59097 3.82979
18 1OS7 AKG 0.0004566 0.453 3.88693
19 1OS7 TAU 0.0004566 0.453 3.88693
20 2JIG PD2 0.0001416 0.41391 4.01786
21 3H7J PPY 0.007014 0.41636 4.11523
22 4JZR 4JR 0.007797 0.42692 4.16667
23 1F6D UDP 0.01281 0.41181 4.25532
24 5EPA AKG 0.0001365 0.41306 4.30108
25 5UQD AKG 0.0000007615 0.4418 4.75113
26 5C5T AKG 0.001706 0.46011 4.82456
27 5F3I 5UJ 0.00000004354 0.66429 5
28 5IQT AKG 0.000365 0.45716 5.07937
29 5IQT 6CU 0.0002985 0.44566 5.07937
30 1J3R 6PG 0.0005932 0.40357 5.26316
31 2GC0 PAN 0.0008073 0.45088 5.31915
32 4ZXA H8N 0.0002705 0.50027 5.35714
33 5HV0 AKG 0.00005064 0.44551 5.52995
34 4MNS 2AX 0.006989 0.42305 5.66038
35 1DZK PRZ 0.01188 0.40206 5.73248
36 2YBP 2HG 0.00000002863 0.72104 5.77428
37 2OS2 OGA 0.00000004391 0.71102 5.77428
38 3KFF XBT 0.01167 0.42266 6.17284
39 3KFF ZBT 0.01167 0.42266 6.17284
40 1GP6 QUE 0.001958 0.42396 6.17978
41 1GP6 SIN 0.002274 0.41962 6.17978
42 1GP6 DH2 0.002274 0.41962 6.17978
43 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.00009638 0.48687 6.19469
44 1N5S ADL 0.013 0.40025 6.25
45 4CCK OGA 0.00002492 0.40771 6.63812
46 4Y3O OGA 0.00002569 0.56541 6.65236
47 4H69 10Y 0.006333 0.41843 6.70103
48 4N7C AEF 0.02553 0.40937 6.81818
49 4IAW LIZ 0.01356 0.4148 7.44681
50 3OPT AKG 0.0000001045 0.69057 7.7748
51 5L9V OGA 0.01109 0.41489 7.93651
52 5L9B AKG 0.01653 0.40635 7.93651
53 3MPB FRU 0.007568 0.41481 8.13008
54 4FE2 AIR 0.01935 0.40297 8.62745
55 4QXB OGA 0.00004431 0.43384 8.82353
56 5I0U DCY 0.0001194 0.42367 9.5
57 4XAC AKG 0.0003178 0.40062 10.3175
58 4QM9 CYS 0.00095 0.47978 10.4046
59 2XUM OGA 0.00003808 0.40648 11.1748
60 5FLJ QUE 0.005464 0.40051 11.2903
61 5IVE 6E8 0.00000007145 0.61889 12.1212
62 4IGQ THR M3L GLN 0.000000651 0.53608 12.5
63 4IGQ OGA 0.00000001548 0.4465 12.5
64 1LRH NLA 0.0001449 0.42154 12.8834
65 4XCB HY0 0.000961 0.43688 16.4751
Pocket No.: 2; Query (leader) PDB : 5FP3; Ligand: 3JI; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 5fp3.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VFT SOR 0.02213 0.40009 1.65877
2 1OJJ GLC GAL 0.02118 0.40499 1.74129
3 3VSV XYP 0.02585 0.40059 3.13725
4 5T7I LAT NAG GAL 0.03208 0.40096 5.16129
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