Receptor
PDB id Resolution Class Description Source Keywords
5A7N 2.39 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 4 HOMO SAPIENS OXIDOREDUCTASE JMJD2A KDM4A
Ref.: DOCKING AND LINKING OF FRAGMENTS TO DISCOVER JUMONJ DEMETHYLASE INHIBITORS. J.MED.CHEM. V. 59 1580 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:1356;
A:1360;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
EDO B:1354;
A:1356;
A:1355;
A:1359;
A:1357;
B:1355;
A:1358;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
ZN A:502;
B:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
VAO B:4001;
A:4000;
Valid;
Valid;
none;
none;
submit data
240.214 C13 H8 N2 O3 c1cc(...
MN B:501;
A:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6H4R 2.14 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN KDM4A IN COMPLEX WITH COMPOUND 17 HOMO SAPIENS HISTONE DEMETHYLASE INHIBITOR TRANSCRIPTION OXIDOREDUCTAS
Ref.: C8-SUBSTITUTED PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONES: S TOWARDS THE IDENTIFICATION OF POTENT, CELL PENETRAN C DOMAIN CONTAINING HISTONE LYSINE DEMETHYLASE 4 SU (KDM4) INHIBITORS, COMPOUND PROFILING IN CELL-BASED ENGAGEMENT ASSAYS. EUR.J.MED.CHEM.
Members (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
70% Homology Family (49)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
39 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
40 4XDO ic50 = 84 uM OGA C4 H5 N O5 C(C(=O)O)N....
41 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
42 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
43 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
44 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
45 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
46 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
47 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
48 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
49 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
39 3OPT - AKG C5 H6 O5 C(CC(=O)O)....
40 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
41 4XDO ic50 = 84 uM OGA C4 H5 N O5 C(C(=O)O)N....
42 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
43 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
44 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
45 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
46 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
47 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
48 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
49 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
50 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VAO; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 VAO 1 1
2 KCH 0.59322 0.805556
3 S2X 0.538462 0.707317
4 35M 0.486111 0.725
Similar Ligands (3D)
Ligand no: 1; Ligand: VAO; Similar ligands found: 111
No: Ligand Similarity coefficient
1 XEV 0.9538
2 0RY 0.9529
3 AV4 0.9514
4 Q4G 0.9467
5 QKU 0.9464
6 L5D 0.9426
7 IQQ 0.9410
8 VM7 0.9294
9 BXZ 0.9277
10 WVV 0.9263
11 EFX 0.9257
12 AUV 0.9223
13 JWS 0.9165
14 1XS 0.9134
15 EAJ 0.9121
16 FC2 0.9109
17 H7S 0.9102
18 7L9 0.9098
19 2UD 0.9095
20 ELH 0.9051
21 ZYW 0.9049
22 3RP 0.9048
23 NIR 0.9046
24 1ER 0.9025
25 II4 0.9022
26 MLO 0.8989
27 1SF 0.8979
28 2GD 0.8949
29 28B 0.8947
30 7G2 0.8938
31 TIA 0.8932
32 Q2S 0.8931
33 4G2 0.8924
34 27M 0.8911
35 0FS 0.8908
36 X29 0.8906
37 YE6 0.8889
38 TVC 0.8877
39 B21 0.8868
40 IA2 0.8865
41 5C1 0.8855
42 5F8 0.8845
43 5FL 0.8842
44 7DE 0.8837
45 2FA 0.8836
46 AMR 0.8832
47 1FL 0.8825
48 HDU 0.8816
49 1AJ 0.8814
50 43U 0.8814
51 R9G 0.8814
52 9RM 0.8813
53 G30 0.8808
54 28A 0.8802
55 6U5 0.8790
56 RFZ 0.8789
57 581 0.8789
58 0LO 0.8782
59 DXK 0.8781
60 BNY 0.8775
61 S8J 0.8764
62 KMG 0.8758
63 272 0.8754
64 B2T 0.8752
65 TJM 0.8751
66 Q92 0.8748
67 AVA 0.8744
68 FCD 0.8741
69 AYN 0.8739
70 7WH 0.8736
71 2LW 0.8735
72 0DJ 0.8734
73 43S 0.8721
74 GLA BEZ 0.8718
75 PZ8 0.8718
76 S1D 0.8704
77 SOV 0.8699
78 X6P 0.8696
79 6PB 0.8695
80 GMP 0.8691
81 JSX 0.8685
82 ARJ 0.8680
83 NOC 0.8680
84 T28 0.8679
85 LLT 0.8676
86 WOE 0.8671
87 NNR 0.8668
88 2QO 0.8667
89 WUB 0.8660
90 2QU 0.8657
91 2GE 0.8644
92 5E4 0.8641
93 OA1 0.8625
94 6EN 0.8620
95 MEX 0.8612
96 NQ7 0.8611
97 NIY 0.8606
98 4UO 0.8602
99 5B2 0.8598
100 BGC GAL 0.8588
101 B4L 0.8564
102 C0H 0.8563
103 LM7 0.8559
104 C0Y 0.8558
105 ABJ 0.8557
106 LL1 0.8552
107 53X 0.8552
108 TLF 0.8550
109 ZME 0.8542
110 6J3 0.8541
111 ID8 0.8540
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6H4R; Ligand: FQB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6h4r.bio4) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6H4R; Ligand: FQB; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 6h4r.bio2) has 60 residues
No: Leader PDB Ligand Sequence Similarity
1 4IGQ OGA 41.3889
2 6IP0 AKG 43.3333
Pocket No.: 3; Query (leader) PDB : 6H4R; Ligand: FQB; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 6h4r.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 6IP0 AKG 43.3333
Pocket No.: 4; Query (leader) PDB : 6H4R; Ligand: FQB; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 6h4r.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 4IGQ OGA 41.3889
2 4IGQ THR M3L GLN 41.3889
3 6IP0 AKG 43.3333
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