Receptor
PDB id Resolution Class Description Source Keywords
5KR7 1.9 Å EC: 1.14.11.- KDM4C BOUND TO PYRAZOLO-PYRIMIDINE SCAFFOLD HOMO SAPIENS INHIBITOR HISTONE LYSINE DEMETHYLASE OXIDOREDUCTASE
Ref.: IDENTIFICATION OF POTENT, SELECTIVE KDM5 INHIBITORS BIOORG.MED.CHEM.LETT. V. 26 4350 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:402;
B:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
6X9 A:403;
B:403;
Valid;
Valid;
none;
none;
ic50 = 2.88 uM
216.239 C11 H12 N4 O CCC1=...
CL B:404;
A:404;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
FE2 B:401;
A:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
55.845 Fe [Fe+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KR7 1.9 Å EC: 1.14.11.- KDM4C BOUND TO PYRAZOLO-PYRIMIDINE SCAFFOLD HOMO SAPIENS INHIBITOR HISTONE LYSINE DEMETHYLASE OXIDOREDUCTASE
Ref.: IDENTIFICATION OF POTENT, SELECTIVE KDM5 INHIBITORS BIOORG.MED.CHEM.LETT. V. 26 4350 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
2 4XDO ic50 = 11 mM OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
2 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
3 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
4 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
5 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
6 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
7 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
8 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
9 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
10 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
11 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
12 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
13 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
14 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
15 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
16 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
17 4URA ic50 = 5.01 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
18 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
19 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
20 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
21 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
22 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
23 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
24 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
25 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
26 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
27 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
28 4XDO ic50 = 11 mM OGA C4 H5 N O5 C(C(=O)O)N....
29 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
30 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
31 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
32 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
33 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
34 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
35 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
36 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
37 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
50% Homology Family (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3OPT - AKG C5 H6 O5 C(CC(=O)O)....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
5 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
6 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
7 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
8 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
9 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
10 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
11 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
12 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
13 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
14 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
15 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
16 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
17 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
18 4URA ic50 = 5.01 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
19 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
20 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
21 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
22 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
23 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
24 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
25 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
26 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
27 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
28 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
29 4XDO ic50 = 11 mM OGA C4 H5 N O5 C(C(=O)O)N....
30 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
31 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
32 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
33 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
34 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
35 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
36 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
37 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
38 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6X9; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 6X9 1 1
2 4VS 0.483333 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KR7; Ligand: 6X9; Similar sites found: 58
This union binding pocket(no: 1) in the query (biounit: 5kr7.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U6R ADP 0.006185 0.41564 1.08992
2 2JIG PD2 0.00162 0.42416 1.33929
3 2XUM OGA 0.000006164 0.48698 1.7192
4 3G5D 1N1 0.02112 0.42623 2.0979
5 1DRY AKG 0.0209 0.40336 2.16049
6 1DRY AAG 0.0209 0.40336 2.16049
7 4EU7 CIT 0.02557 0.41124 2.17984
8 3KV5 OGA 0.00002136 0.54967 2.7248
9 3KV4 OGA 0.0001041 0.45938 2.7248
10 2RDQ AKG 0.002155 0.44309 2.77778
11 4YRD 3IT 0.0004078 0.47303 2.78552
12 5I0U DCY 0.0004382 0.4546 3
13 4GJY OGA 0.000001156 0.61712 3.40426
14 3PUR 2HG 0.00007215 0.52174 3.78788
15 3N9O OGA 0.00004264 0.45986 3.78788
16 3N9Q OGA 0.00004492 0.45954 3.78788
17 3N9P OGA 0.00005043 0.45799 3.78788
18 5UQD AKG 0.00001226 0.47359 3.81471
19 3ZDS HMQ 0.001465 0.43159 3.81471
20 3ZDS HQ9 0.001297 0.418 3.81471
21 3ZDS M8O 0.002925 0.41298 3.81471
22 3ZDS OMD 0.003435 0.41089 3.81471
23 1ODM ASV 0.008237 0.42022 3.92749
24 5TFZ 7BC 0.001706 0.42288 4
25 1USF NAP 0.02467 0.40474 4.49438
26 4ZXA H8N 0.005279 0.42138 4.7619
27 5M0T AKG 0.02001 0.40106 4.7619
28 4WVW SLT 0.0153 0.40037 4.86111
29 3PUA OGA 0.0005861 0.42884 4.90463
30 4WOE ADP 0.01385 0.40928 4.90463
31 4XAC AKG 0.00146 0.41465 5.15873
32 4Y3O OGA 0.0002315 0.49458 5.17711
33 5HV0 AKG 0.0002279 0.47756 5.52995
34 3B6R ADP 0.004135 0.42171 5.72207
35 1AJS PLA 0.01812 0.40213 5.72207
36 3MTX PGT 0.03019 0.40034 5.96026
37 4TW7 37K 0.003113 0.44225 6.25
38 4J25 OGA 0.005336 0.42773 6.9869
39 4QXB OGA 0.000007986 0.52393 7.29483
40 1LRH NLA 0.004609 0.40234 7.36196
41 5C5T AKG 0.01074 0.40645 7.45614
42 2OQ2 A3P 0.005098 0.4287 8.04598
43 3QP8 HL0 0.007458 0.40979 8.15217
44 5IXH OTP 0.02392 0.41547 8.69565
45 4YRY NAD 0.04477 0.40534 9.05797
46 4QM9 CYS 0.001665 0.45281 9.24856
47 4CCK OGA 0.0002065 0.43185 9.53679
48 5EPA AKG 0.003973 0.40286 9.67742
49 2Y6Q I7T 0.04945 0.40305 9.80926
50 2GJ5 VD3 0.01903 0.41583 9.87654
51 1W6O LAT 0.01202 0.40765 10.4478
52 3L9R L9Q 0.01918 0.41248 14.2857
53 3L9R L9R 0.02512 0.4097 14.2857
54 4QYN RTL 0.01411 0.40581 14.2857
55 1KGI T4A 0.006472 0.42371 14.9606
56 4IGQ THR M3L GLN 0.0000002674 0.6228 41.1111
57 4IGQ OGA 0.0000000001801 0.58756 41.1111
58 5IVE 6E8 0.0000000002298 0.7993 47.5758
Pocket No.: 2; Query (leader) PDB : 5KR7; Ligand: 6X9; Similar sites found: 36
This union binding pocket(no: 2) in the query (biounit: 5kr7.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2OFV 242 0.02059 0.41574 2.16606
2 1OUK 084 0.0234 0.44787 2.18579
3 5JKG 6LF 0.02752 0.41126 2.2508
4 5HES 032 0.008922 0.41954 2.28013
5 2XMY CDK 0.008396 0.45716 2.34899
6 5HCY 60D 0.005997 0.45067 2.45232
7 4P8K FAD 0.04647 0.4146 2.45232
8 4P8K 38C 0.04767 0.4146 2.45232
9 5N87 N66 0.02503 0.41136 2.55591
10 5UR1 YY9 0.02871 0.40383 2.89389
11 5LIA 6XN 0.01564 0.44429 2.99728
12 4BKJ STI 0.01266 0.41514 3.1746
13 5FLJ QUE 0.01555 0.40604 3.22581
14 5H2U 1N1 0.009485 0.41298 3.37079
15 1RE8 BD2 0.01105 0.43857 3.42857
16 2GU8 796 0.04063 0.41454 3.56083
17 3DLG GWE 0.03685 0.42139 3.81471
18 4HIA FMN 0.01779 0.41901 3.97727
19 5JFS 6K0 0.04265 0.40317 4.22078
20 3E85 BSU 0.02882 0.41214 4.43038
21 1ZB6 GST 0.007718 0.43153 4.56026
22 4PVD NDP 0.02407 0.40398 4.67836
23 2B4Q NAP 0.02304 0.40872 4.71014
24 1KNR FAD 0.04545 0.40348 4.90463
25 4D4U FUC GAL 0.01299 0.41081 5.39683
26 5D48 L96 0.02612 0.40086 5.92105
27 5IE3 AMP 0.02133 0.40921 6.81199
28 5IE3 OXD 0.02133 0.40921 6.81199
29 4IAW LIZ 0.00942 0.40243 7.97872
30 1QKQ MAN 0.001093 0.44327 8.4507
31 1VJY 460 0.005886 0.44008 9.24092
32 2HK5 1BM 0.01425 0.4062 10
33 5W4W 9WG 0.01047 0.41772 10.574
34 5DKK FMN 0.00502 0.42825 12.4138
35 4X6F 3XU 0.03114 0.41038 15.2381
36 5LJB RTL 0.01584 0.40395 15.5556
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