Receptor
PDB id Resolution Class Description Source Keywords
5F5C 1.88 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JMJD2D COMPLEXED WITH KDOPP7 HOMO SAPIENS DOUBLE-STRANDED BETA HELIX DEMETHYLASE OXYGENASE OXIDOREDSTRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC
Ref.: 8-SUBSTITUTED PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONE DERI AS POTENT, CELL PERMEABLE, KDM4 (JMJD2) AND KDM5 (J HISTONE LYSINE DEMETHYLASE INHIBITORS. J.MED.CHEM. V. 59 1388 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI A:402;
 Part of Protein;
 none;
 submit data
58.693 Ni [Ni+2...
EDO A:404;
A:410;
A:405;
A:406;
A:403;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
ZN A:401;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
SO4 A:408;
A:409;
A:407;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
96.063 O4 S [O-]S...
5V3 A:411;
 Valid;
 none;
 submit data
266.298 C15 H14 N4 O c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FP4 2 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-(4- PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLIC ACID HOMO SAPIENS TRANSCRIPTION INHIBITOR LYSINE SPECIFIC HISTONE DEMETHYLASJMJD2D KDM4D 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 (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
2 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
3 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
4 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
5 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
6 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
7 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
8 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
9 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
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: 5V3; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 5V3 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 5V3; Similar ligands found: 92
No: Ligand Similarity coefficient
1 0RU 0.9253
2 9RK 0.9207
3 87F 0.9181
4 4KN 0.9163
5 8WW 0.9143
6 KWK 0.9138
7 SCE 0.9136
8 MF5 0.9113
9 EBB 0.9111
10 5V0 0.9107
11 PV1 0.9094
12 BBO 0.9063
13 HN3 0.9058
14 JXB 0.9052
15 4P9 0.9042
16 0QX 0.9041
17 5HG 0.9034
18 X8W 0.9026
19 4YE 0.9009
20 M0V 0.9008
21 5RW 0.9005
22 00G 0.9005
23 M00 0.9001
24 G27 0.8998
25 100 0.8997
26 873 0.8997
27 41L 0.8981
28 G50 0.8978
29 JYQ 0.8974
30 KTV 0.8970
31 QDR 0.8963
32 HN2 0.8959
33 4YF 0.8943
34 PNX 0.8939
35 L81 0.8931
36 INI 0.8907
37 1UA 0.8895
38 FIP 0.8894
39 IGP 0.8891
40 2BI 0.8883
41 IPL 0.8882
42 5EZ 0.8869
43 QUG 0.8866
44 7NC 0.8866
45 M0S 0.8865
46 21X 0.8849
47 X2L 0.8847
48 ON1 0.8841
49 QEI 0.8838
50 F0C 0.8829
51 ALJ 0.8820
52 M0M 0.8814
53 BFS 0.8809
54 2DT 0.8800
55 3G3 0.8796
56 OA5 0.8789
57 IAG 0.8783
58 F91 0.8772
59 BXB 0.8771
60 JCQ 0.8769
61 YC8 0.8762
62 AX8 0.8762
63 P1Y 0.8748
64 9D9 0.8742
65 WDU 0.8742
66 TRP GLY 0.8735
67 GYZ 0.8730
68 4JV 0.8722
69 HA1 0.8717
70 GU7 0.8712
71 JYE 0.8710
72 PV2 0.8709
73 HFS 0.8694
74 F6W 0.8688
75 FR2 0.8682
76 JWW 0.8678
77 M62 0.8661
78 8MF 0.8658
79 UN4 0.8657
80 9ME 0.8630
81 KVQ 0.8629
82 KSY 0.8624
83 TCW 0.8621
84 7BH 0.8616
85 A0R 0.8609
86 CMG 0.8592
87 LI4 0.8591
88 9MK 0.8573
89 TMP 0.8550
90 LFK 0.8544
91 M1D 0.8535
92 RNB 0.8530
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FP4; Ligand: YC8; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5fp4.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 6IP0 AKG 43.7126
Pocket No.: 2; Query (leader) PDB : 5FP4; Ligand: YC8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5fp4.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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