Receptor
PDB id Resolution Class Description Source Keywords
5FWJ 2.1 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JARID1C IN COMPLEX WITH KDM5-C49 HOMO SAPIENS OXIDOREDUCTASE LYSINE-SPECIFIC LYSINE-SPECIFIC DEMETHYLASE
Ref.: STRUCTURAL ANALYSIS OF HUMAN KDM5B GUIDES HISTONE DEMETHYLASE INHIBITOR DEVELOPMENT. NAT.CHEM.BIOL. V. 12 539 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MMK B:1775;
A:1775;
Valid;
Valid;
none;
none;
Ki = 0.0061 uM
306.36 C15 H22 N4 O3 CCN(/...
MN A:1772;
B:1772;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
MG A:1773;
A:805;
B:1774;
A:1774;
B:1773;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
ZN A:1770;
B:1770;
A:1771;
B:1771;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FWJ 2.1 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JARID1C IN COMPLEX WITH KDM5-C49 HOMO SAPIENS OXIDOREDUCTASE LYSINE-SPECIFIC LYSINE-SPECIFIC DEMETHYLASE
Ref.: STRUCTURAL ANALYSIS OF HUMAN KDM5B GUIDES HISTONE DEMETHYLASE INHIBITOR DEVELOPMENT. NAT.CHEM.BIOL. V. 12 539 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
2 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
3 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
4 5FPL - MN QAY n/a n/a
5 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
6 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
7 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
9 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
10 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
2 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
3 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
4 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
5 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
6 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
7 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
8 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
9 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
10 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
11 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
12 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
13 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
14 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
15 5FPL - MN QAY n/a n/a
16 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
17 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
18 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
19 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
20 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
21 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
22 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
23 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MMK; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 MMK 1 1
2 LQT 0.466667 0.796296
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FWJ; Ligand: MMK; Similar sites found: 69
This union binding pocket(no: 1) in the query (biounit: 5fwj.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4K3H 1OM 0.006278 0.42815 None
2 4WCX MET 0.0057 0.42691 1.91083
3 5LUN OGA 0.001149 0.44291 1.98864
4 5LUN ARG 0.005328 0.44005 1.98864
5 2RKV COA 0.04545 0.40039 1.99557
6 3KV5 OGA 0.0002713 0.48207 2.12314
7 5C5H 4YB 0.03362 0.40035 2.20751
8 3KV4 OGA 0.002414 0.41946 2.23714
9 4J4H 1J1 0.04566 0.4351 2.3166
10 4J4H NAI 0.01772 0.43265 2.3166
11 2J3M ATP 0.00934 0.42297 2.33546
12 2J3M PRI 0.01574 0.41307 2.33546
13 4TW7 37K 0.02364 0.40692 2.34375
14 1ODM ASV 0.003287 0.44915 2.41692
15 4GJY OGA 0.000001539 0.60339 2.55319
16 3MTX PGT 0.02413 0.41275 2.64901
17 3PUR 2HG 0.0002653 0.48795 2.76008
18 3N9O OGA 0.001849 0.41345 2.76008
19 3N9Q OGA 0.002003 0.41214 2.76008
20 3N9P OGA 0.002014 0.41095 2.76008
21 4CCK OGA 0.00002521 0.4875 2.99786
22 4Y3O OGA 0.00002967 0.53645 3.00429
23 1J3R 6PG 0.001327 0.44764 3.15789
24 3FW4 CAQ 0.01681 0.41453 3.37079
25 4ZXA H8N 0.004385 0.42011 3.53982
26 5UQD AKG 0.001583 0.41464 3.61991
27 5HV0 AKG 0.000188 0.49406 3.68664
28 2FCU AKG 0.004998 0.40356 3.83387
29 4YRD 3IT 0.002117 0.43779 3.89972
30 5JSP DQY 0.003458 0.41353 3.9801
31 5TFZ 7BC 0.0006242 0.46035 4
32 5IXH OTP 0.03293 0.41549 4.34783
33 3E85 BSU 0.02515 0.4191 4.43038
34 4ZU4 4TG 0.01885 0.40253 4.72973
35 4XAC AKG 0.004823 0.40594 4.7619
36 5C5T AKG 0.0004605 0.46662 4.82456
37 4YVN EBS 0.01201 0.40757 5.09554
38 4HIA FMN 0.01428 0.42811 5.11364
39 2RDQ AKG 0.00128 0.4645 5.20833
40 2NNQ T4B 0.01878 0.42493 5.34351
41 3PUA OGA 0.00008064 0.48587 5.35714
42 5C3R AKG 0.0007114 0.41657 5.53936
43 5C3R HMU 0.0007114 0.41657 5.53936
44 1OIJ AKG 0.001446 0.40541 5.98007
45 5FLJ QUE 0.02137 0.40479 6.45161
46 2CM4 RCL 0.02116 0.40343 6.66667
47 3ACL 3F1 0.003869 0.43252 6.75676
48 1LSH PLD 0.01951 0.41517 6.89655
49 1GP6 QUE 0.001424 0.46925 7.02247
50 1GP6 SIN 0.00132 0.46925 7.02247
51 1GP6 DH2 0.00132 0.46925 7.02247
52 4QXB OGA 0.0006399 0.45983 7.35294
53 2FB3 GTP 0.009983 0.43026 7.35294
54 4ZU5 THM 0.01757 0.40028 7.63889
55 4J25 OGA 0.0005971 0.4704 7.86026
56 2JIG PD2 0.0001095 0.49625 8.03571
57 1DRY AKG 0.02208 0.40981 8.33333
58 1DRY AAG 0.02208 0.40981 8.33333
59 5I0U DCY 0.0002584 0.48166 9
60 4XCB AKG 0.002269 0.42764 9.1954
61 4XCB HY0 0.0105 0.425 9.1954
62 5J8O 6GZ 0.009987 0.41234 10.4839
63 4QM9 CYS 0.0008956 0.46207 13.8728
64 1LRH NLA 0.003214 0.42924 14.7239
65 4F7E 0SH 0.01988 0.42457 16.3265
66 3OPT AKG 0.0000000456 0.67722 42.0912
67 2OS2 OGA 0.00000001718 0.69901 42.2572
68 2YBP 2HG 0.00000002606 0.68951 42.2572
69 5F3I 5UJ 0.00000001181 0.7758 44.7222
70 2XUM OGA 0.00001156 0.50141 50
Pocket No.: 2; Query (leader) PDB : 5FWJ; Ligand: MMK; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 5fwj.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2RKV ZBA 0.02468 0.4176 1.99557
2 5FSY AR6 0.02174 0.40283 3.00752
3 2WSA 646 0.02372 0.44517 3.39703
4 2WSA MYA 0.02372 0.44517 3.39703
5 2GC0 PAN 0.002552 0.40013 4.25532
6 4WN5 MVC 0.02497 0.40135 5.21739
7 1N07 FMN 0.0356 0.40497 8.58896
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