Receptor
PDB id Resolution Class Description Source Keywords
4HON 1.8 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JMJD2D/KDM4D IN COMPLEX WITH AN H PEPTIDE AND 2-OXOGLUTARATE HOMO SAPIENS JUMONJI C DEMETHYLASE JMJD2/KDM4 FAMILY BETA BARREL FOLD OXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL ANALYSIS OF JMJD2D REVEAL MOLECULAR BASIS FOR SITE-SPECIFIC DEMETHYLATION AMO DEMETHYLASES. STRUCTURE V. 21 98 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
146.098 C5 H6 O5 C(CC(...
NI A:402;
B:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
NO3 A:407;
A:408;
A:409;
A:410;
A:411;
A:412;
A:413;
A:414;
B:407;
B:408;
B:409;
B:410;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.005 N O3 [N+](...
PDO A:415;
A:416;
A:417;
A:418;
B:411;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
76.094 C3 H8 O2 C(CO)...
SCN A:404;
A:405;
A:406;
B:404;
B:405;
B:406;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
58.082 C N S C(#N)...
THR ALA ARG M3L SER THR GLY GLY LYS ALA F:6;
G:7;
Valid;
Valid;
none;
none;
submit data
948.114 n/a O=C(N...
ZN A:403;
B:403;
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
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 26 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 (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: AKG; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 OOG 0.5 0.947368
3 69O 0.458333 0.714286
4 2IT 0.423077 0.615385
5 SHF 0.416667 0.666667
6 3PY 0.409091 0.652174
Ligand no: 2; Ligand: THR ALA ARG M3L SER THR GLY GLY LYS ALA; Similar ligands found: 43
No: Ligand ECFP6 Tc MDL keys Tc
1 THR ALA ARG M3L SER THR GLY GLY LYS ALA 1 1
2 LYS GLN THR ALA ARG M3L SER THR GLY 0.714286 1
3 ALA ARG M3L SER THR GLY GLY ALY 0.624 0.96875
4 LYS ALA ALA ARG M3L SER ALA 0.579832 0.967742
5 GLN THR ALA ARG M3L SER THR GLY 0.570312 1
6 THR ALA ARG MYK SER THR GLY 0.557252 0.84375
7 PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP 0.532051 0.72
8 GLN THR ALA ARG MYK SER THR GLY GLY TRP 0.532051 0.72
9 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.512195 0.983871
10 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.512195 0.983871
11 ALA ARG THR M3L GLN THR ALA 0.512195 0.983871
12 ALA ARG MLZ SER THR GLY GLY ALY 0.507463 0.875
13 ALA ARG MLY SER THR GLY GLY ALY 0.503704 0.9375
14 ARG GLY PHE ALA LEU M3L SER THR HIS GLY 0.484277 0.837838
15 ALA GLN THR ALA ARG ALY SER THR 0.481203 0.854839
16 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.480315 0.806452
17 ALA ARG THR M3L GLN THR ALA ARG 0.469231 0.968254
18 ALA ALA LEU THR ARG ALA 0.467213 0.774194
19 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.466667 0.968254
20 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.466216 0.983871
21 ALA ARG THR M3L GLN THR ALA ARG LYS 0.460938 0.983871
22 ACE GLN THR ALA ARG KCR SER THR 0.457143 0.825397
23 ALA ARG M3L SER CYS GLY GLY LYS 08P 0.455782 0.884058
24 ALA ARG M3L SER 0.452991 0.935484
25 ALA ARG LYS SEP THR GLY GLY LYS 0.449275 0.779412
26 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.449153 0.806452
27 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.447552 0.983871
28 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.445312 0.698413
29 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.440559 0.983871
30 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.429752 0.854839
31 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.424837 0.764706
32 ALA ARG THR ALY GLN THR ALA 0.423077 0.83871
33 VAL ALA ARG SER 0.421053 0.714286
34 SER THR GLY GLY VAL M3L LYS PRO HIS ARG 0.41573 0.826667
35 LEU GLU LYS ALA ARG GLY SER THR TYR 0.411392 0.757143
36 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.409091 0.951613
37 ALA ARG THR MLY GLN THR ALA 0.409091 0.951613
38 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.406667 0.638889
39 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.404762 0.84127
40 ASN ARG LEU LEU LEU THR GLY 0.401639 0.793651
41 ALA ARG THR LYS GLN THR ALA ARG 0.4 0.806452
42 THR ALA ARG M3L SER THR 0.4 0.935484
43 ALA ARG THR LYS GLN THR ALA ARG LYS 0.4 0.806452
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FP4; Ligand: YC8; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5fp4.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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