Receptor
PDB id Resolution Class Description Source Keywords
5IW0 1.63 Å EC: 2.1.14.11 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N19 [2-(5-((4 METHYLBENZYL)OXY)-1H-PYRAZOL-1-YL)ISONICOTINIC ACID] HOMO SAPIENS DEMETHYLASE INHIBITION OXIDOREDUCTASE-OXIDOREDUCTASE INHIBICOMPLEX
Ref.: STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLA INHIBITION BY DIVERSE COMPOUNDS. CELL CHEM BIOL V. 23 769 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:607;
A:606;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
EDO A:605;
A:604;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
AKG A:602;
Valid;
Atoms found MORE than expected: % Diff = 2;
submit data
146.098 C5 H6 O5 C(CC(...
MN A:603;
Invalid;
none;
submit data
54.938 Mn [Mn+2...
6EP A:601;
Valid;
none;
Kd = 0.06 uM
343.764 C17 H14 Cl N3 O3 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IVE 1.78 Å EC: 2.1.14.11 LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N8 ( 5-METHYL (PROPAN-2-YL)-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBON HOMO SAPIENS DEMETHYLASE INHIBITION OXIDOREDUCTASE-OXIDOREDUCTASE INHIBICOMPLEX
Ref.: STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLA INHIBITION BY DIVERSE COMPOUNDS. CELL CHEM BIOL V. 23 769 2016
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
2 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
3 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
4 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
5 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
6 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
7 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
8 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
9 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
10 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
11 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
2 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
3 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
4 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
5 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
6 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
7 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
8 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
9 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
10 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
11 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
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: 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: 6EP; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 6EP 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IVE; Ligand: 6E8; Similar sites found: 87
This union binding pocket(no: 1) in the query (biounit: 5ive.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SN0 T44 0.01062 0.42175 None
2 1DRY AAG 0.003118 0.40938 1.23457
3 1DRY AKG 0.003118 0.40938 1.23457
4 5C3R HMU 0.005851 0.42282 1.81818
5 5C3R AKG 0.005851 0.42282 1.81818
6 3W21 AKG 0.01349 0.42504 1.8315
7 4BQY FNT 0.002574 0.43175 1.98413
8 5L9V OGA 0.01672 0.41581 1.98413
9 5L9B AKG 0.0275 0.40479 1.98413
10 3HQR OGA 0.02208 0.40597 2.03252
11 5LUN OGA 0.005296 0.45085 2.12121
12 4FFG 0U8 0.01089 0.4342 2.12121
13 4WOE ADP 0.02068 0.42089 2.12121
14 2HBL AMP 0.03551 0.41347 2.12121
15 2WBP ZZU 0.009018 0.40163 2.12121
16 2WBP SIN 0.009018 0.40163 2.12121
17 3JRX S1A 0.01729 0.40101 2.12121
18 4QM9 CYS 0.00225 0.47248 2.31214
19 1OIJ AKG 0.01553 0.42175 2.32558
20 4ZNO SUC 0.029 0.40736 2.42424
21 5F6U 5VK 0.007086 0.44437 2.54777
22 1WLJ U5P 0.02287 0.42148 2.6455
23 2GC0 PAN 0.00362 0.43245 3.19149
24 4IAW LIZ 0.02184 0.40991 3.19149
25 4YVN EBS 0.004434 0.45884 3.33333
26 4ZXA H8N 0.004734 0.44834 3.33333
27 3HQP OXL 0.01776 0.42394 3.33333
28 4OUC 5ID 0.008909 0.4216 3.33333
29 4IMO PWZ 0.03368 0.41136 3.40909
30 4MTI 2DX 0.0455 0.40228 3.47826
31 5C5T AKG 0.001148 0.48016 3.50877
32 5F7U GLC GLC 0.04286 0.40515 3.63636
33 1QGQ UDP 0.03261 0.40472 3.92157
34 4YRD 3IT 0.002209 0.45976 3.93939
35 5OO5 UUA 0.01826 0.40311 4.03226
36 4CC6 L5Y 0.01893 0.41708 4.08805
37 2ZBA ZBA 0.02603 0.40241 4.13943
38 2OFE NAG 0.02883 0.41311 4.22535
39 4IE6 UN9 0.002383 0.41121 4.24242
40 3FW9 SLX 0.01251 0.40433 4.24242
41 4J25 OGA 0.004631 0.45528 4.36681
42 2JIG PD2 0.001181 0.47953 4.46429
43 4GQP B40 0.01354 0.4295 4.81928
44 5UQD AKG 0.0008341 0.49799 4.84848
45 4OCT AKG 0.001752 0.46537 5.40541
46 4Y3O OGA 0.0001935 0.52951 5.45455
47 5BTX CMP 0.01687 0.41282 5.47945
48 1LRH NLA 0.0009483 0.47882 5.52147
49 1J3R 6PG 0.001204 0.47359 5.78947
50 1O4T OXL 0.02323 0.41221 6.01504
51 5HVJ ANP 0.03277 0.40408 6.03175
52 2P3I MNA 0.01346 0.42702 6.21118
53 2HRL SIA GAL SIA BGC NGA CEQ 0.03356 0.40407 6.29921
54 4LOC OXM 0.01699 0.40752 6.36364
55 3E2M E2M 0.002663 0.41794 6.48649
56 3MPB FRU 0.01005 0.41906 6.50407
57 3H7J PPY 0.01521 0.41034 6.58436
58 5FUI APY 0.003336 0.46024 6.81818
59 4JX1 CAM 0.0453 0.40242 6.9697
60 1QKQ MAN 0.002643 0.42858 7.04225
61 4Z2S NAG 0.03062 0.41153 7.04225
62 4Z2S NDG 0.03062 0.41153 7.04225
63 5TFZ 7BC 0.001095 0.48124 8
64 3PUR 2HG 0.0005478 0.50496 8.78788
65 5IQT AKG 0.004781 0.41983 9.20635
66 5IQT 6CU 0.006689 0.40428 9.20635
67 4PEG 5GP 0.04256 0.40341 10.303
68 4YEE 4CQ 0.04185 0.40375 11.1111
69 5FP3 3JI 0.00000007145 0.61889 12.1212
70 4GJY OGA 0.000007392 0.60685 12.3404
71 4QXB OGA 0.0001295 0.52915 17.6471
72 3KV5 OGA 0.0001187 0.53883 18.7879
73 3AVR OGA 0.0000001574 0.69903 19.0909
74 3AVS OGA 0.000001 0.42203 19.0909
75 1N5S ADL 0.00851 0.41883 19.6429
76 4BXF AKG 0.0002459 0.52466 26.3158
77 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.0005726 0.46493 26.5487
78 3OPT AKG 0.0000002835 0.68377 46.9697
79 5KR7 6X9 0.0000000002298 0.7993 47.5758
80 2Q8C AKG 0.00000000971 0.7707 47.8788
81 5LY2 OGA 0.00000001294 0.76294 47.8788
82 5FWE OGA 0.00000001326 0.76293 47.8788
83 2Q8E OGA 0.00000004269 0.72936 47.8788
84 2YBP 2HG 0.00000004998 0.72544 47.8788
85 2OS2 OGA 0.00000005616 0.72279 47.8788
86 5F3I 5UJ 0.0000001432 0.59943 47.8788
87 2P5B OGA 0.0000002357 0.46195 47.8788
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