Receptor
PDB id Resolution Class Description Source Keywords
5ivv 1.85 Å EC: 1.14.11.- LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N12 [3-((1-ME PYRROLO[2,3-B]PYRIDIN-3-YL)AMINO)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
MN A:602;
 Invalid;
 none;
 submit data
54.938 Mn [Mn+2...
6EN A:601;
 Valid;
 none;
 Kd = 0.45 uM
268.271 C14 H12 N4 O2 Cn1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5IVE 1.78 Å EC: 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 (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
2 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
3 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
4 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
5 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
6 6DQ5 Kd = 6.4 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
7 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
8 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
9 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
10 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
11 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
12 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
13 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
14 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
15 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
16 6DQ6 Kd = 8.5 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
17 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
18 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
19 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
20 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
21 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
22 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
23 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
24 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
25 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
26 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
27 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
28 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
70% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
2 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
3 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
4 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
5 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
6 6DQ5 Kd = 6.4 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
7 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
8 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
9 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
10 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
11 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
12 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
13 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
14 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
15 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
16 6DQ6 Kd = 8.5 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
17 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
18 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
19 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
20 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
21 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
22 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
23 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
24 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
25 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
26 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
27 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
28 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
50% Homology Family (44)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 6H51 Ki = 0.016 uM FQK C20 H24 N6 O c1cnc(c2c1....
2 6H4Z Ki = 0.002 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
3 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
4 6H52 ic50 = 0.068 uM FQN C20 H24 N6 O c1cnc(c2c1....
5 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
6 6H50 ic50 = 0.156 uM FO2 C16 H18 N6 O CN1CCC(CC1....
7 5FPL - MN QAY n/a n/a
8 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
9 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
10 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
11 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
12 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
13 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
14 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
15 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
16 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
17 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
18 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
19 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
20 6DQ5 Kd = 6.4 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
21 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
22 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
23 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
24 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
25 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
26 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
27 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
28 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
29 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
30 6DQ6 Kd = 8.5 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
31 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
32 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
33 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
34 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
35 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
36 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
37 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
38 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
39 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
40 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
41 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
42 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
43 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
44 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6EN; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 6EN 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 6EN; Similar ligands found: 188
No: Ligand Similarity coefficient
1 BNY 0.9491
2 ID8 0.9412
3 FLF 0.9407
4 TLF 0.9385
5 CJZ 0.9356
6 145 0.9298
7 4GU 0.9279
8 6J3 0.9251
9 JMS 0.9214
10 581 0.9147
11 PCQ 0.9124
12 BZC 0.9103
13 17C 0.9086
14 BGC BGC 0.9077
15 53X 0.9075
16 SA0 0.9072
17 9CE 0.9055
18 ELH 0.9048
19 XEV 0.9040
20 MHB 0.9038
21 5E4 0.9034
22 NFL 0.9031
23 M0Y 0.9023
24 Q11 0.9023
25 C5Q 0.9016
26 SQM 0.9015
27 MHD GAL 0.8997
28 BGC GAL 0.8995
29 9MR 0.8995
30 U98 0.8995
31 ABL 0.8989
32 SHG BGC 0.8976
33 U19 0.8976
34 6QT 0.8974
35 Z2T 0.8973
36 BGC Z9D 0.8971
37 4K2 0.8969
38 IFM BMA 0.8968
39 BMA IFM 0.8968
40 BGC OXZ 0.8962
41 GCS GCS 0.8960
42 IMB 0.8958
43 NOY BGC 0.8958
44 DMB 0.8950
45 6GR 0.8944
46 EAJ 0.8935
47 IFM BGC 0.8932
48 43S 0.8928
49 IXM 0.8925
50 2QV 0.8925
51 Z16 0.8922
52 NOC 0.8922
53 AV4 0.8920
54 3D8 0.8912
55 AVX 0.8906
56 2GD 0.8906
57 NPZ 0.8901
58 7FZ 0.8897
59 4L2 0.8894
60 683 0.8892
61 38E 0.8888
62 9FN 0.8882
63 BMA BGC 0.8879
64 MTB 0.8869
65 BMA GAL 0.8860
66 ARJ 0.8859
67 2QU 0.8855
68 0FS 0.8853
69 4G2 0.8852
70 I0D 0.8851
71 DS8 0.8849
72 C4E 0.8843
73 6PB 0.8841
74 ISX 0.8838
75 MAN BMA 0.8835
76 NQ7 0.8832
77 NE2 0.8830
78 LI4 0.8828
79 NW1 0.8825
80 PA1 GCS 0.8823
81 IQQ 0.8819
82 BMA BMA 0.8818
83 AYS 0.8817
84 QC1 0.8816
85 XYS XYS 0.8812
86 F40 0.8800
87 3WO 0.8800
88 3WN 0.8800
89 CC6 0.8798
90 EFX 0.8798
91 MR6 0.8794
92 Q4G 0.8784
93 3Q0 0.8782
94 ZYW 0.8782
95 GLC GLC 0.8773
96 GLC GAL 0.8773
97 L5D 0.8772
98 NAB 0.8772
99 Q92 0.8771
100 C0H 0.8770
101 AUY 0.8768
102 NU3 0.8768
103 DXK 0.8765
104 8M5 0.8760
105 TVC 0.8760
106 Z57 0.8756
107 DBS 0.8753
108 5P7 0.8746
109 0RY 0.8744
110 DSQ 0.8743
111 XIL 0.8739
112 3F4 0.8738
113 3RP 0.8736
114 XDL XYP 0.8732
115 6BK 0.8732
116 B4L 0.8731
117 CMG 0.8728
118 BXZ 0.8728
119 XYP XDN 0.8727
120 1ZC 0.8726
121 IMK 0.8725
122 5S9 0.8723
123 SZ5 0.8720
124 25F 0.8717
125 DFL 0.8716
126 MRI 0.8714
127 QLH 0.8712
128 BQZ 0.8711
129 12R 0.8709
130 88X 0.8707
131 FUC GAL 0.8706
132 3B4 0.8696
133 FRU GAL 0.8695
134 BBY 0.8691
135 Z15 0.8689
136 ACK 0.8689
137 WCU 0.8680
138 XDN XYP 0.8679
139 RGK 0.8677
140 97K 0.8674
141 M0Z 0.8672
142 LU2 0.8667
143 GAL GLA 0.8661
144 1FL 0.8657
145 20D 0.8656
146 43U 0.8649
147 5P3 0.8648
148 P4L 0.8640
149 AUV 0.8638
150 AJD 0.8638
151 4ZF 0.8633
152 GHA 0.8630
153 BGC GLA 0.8628
154 833 0.8626
155 VAO 0.8620
156 MYC 0.8620
157 TH1 0.8620
158 1V8 0.8616
159 2BE 0.8616
160 WLH 0.8615
161 6ZW 0.8615
162 O9Q 0.8614
163 TCC 0.8613
164 CFK 0.8610
165 FHI 0.8610
166 UN4 0.8608
167 P2C 0.8603
168 VT3 0.8601
169 1SF 0.8600
170 Q9T 0.8597
171 6DQ 0.8595
172 TIA 0.8591
173 5AV 0.8591
174 OUG 0.8589
175 MBG GLA 0.8588
176 M3W 0.8584
177 0SY 0.8582
178 DGO Z61 0.8579
179 67B 0.8568
180 5NN 0.8563
181 1Q4 0.8560
182 6H2 0.8560
183 3WK 0.8556
184 7ZO 0.8552
185 EAT 0.8551
186 UX0 0.8539
187 OUA 0.8537
188 28A 0.8520
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5IVE; Ligand: 6E8; 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: 5ive.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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