Receptor
PDB id Resolution Class Description Source Keywords
5fp8 1.98 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4- METHYLTHIOPHEN-2-YLMETHYLAMINOPYRIDINE-4-CARBOXYLIC ACID HOMO SAPIENS OXIDOREDUCTASE INHIBITOR LYSINE SPECIFIC HISTONE DEMETHYLAJMJD2D 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1342;
A:1346;
A:1344;
A:1345;
A:1347;
A:1343;
A:1348;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
AUY A:1341;
 Valid;
 none;
 submit data
248.301 C12 H12 N2 O2 S Cc1cc...
CO A:360;
 Part of Protein;
 none;
 submit data
58.933 Co [Co+2...
ZN A:350;
 Part of Protein;
 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 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: AUY; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 AUY 1 1
2 QC1 0.492537 0.717391
Similar Ligands (3D)
Ligand no: 1; Ligand: AUY; Similar ligands found: 298
No: Ligand Similarity coefficient
1 FUZ 0.9681
2 12R 0.9465
3 HHV 0.9461
4 9E3 0.9442
5 DFL 0.9415
6 MHB 0.9396
7 CMG 0.9391
8 AEY 0.9390
9 1BD 0.9366
10 20D 0.9345
11 Q5M 0.9332
12 EMU 0.9329
13 NKI 0.9329
14 1V1 0.9327
15 A73 0.9325
16 5AV 0.9315
17 SQM 0.9298
18 25F 0.9289
19 SZ5 0.9288
20 H35 0.9279
21 ZEA 0.9261
22 3F4 0.9258
23 RGK 0.9253
24 UN4 0.9219
25 A4V 0.9212
26 3D8 0.9210
27 TH4 0.9205
28 08C 0.9168
29 1UZ 0.9163
30 M3W 0.9156
31 HO6 0.9156
32 MRE 0.9155
33 AYS 0.9145
34 MBP 0.9137
35 ON1 0.9128
36 ZRL 0.9119
37 WLH 0.9108
38 3AK 0.9106
39 1XF 0.9106
40 E9L 0.9104
41 VT3 0.9091
42 27F 0.9088
43 NW1 0.9086
44 LI4 0.9084
45 U8K 0.9081
46 F18 0.9081
47 5E4 0.9080
48 AVX 0.9079
49 FNA 0.9075
50 A63 0.9073
51 6J5 0.9072
52 W8L 0.9067
53 AOY 0.9066
54 OSB 0.9064
55 CDJ 0.9062
56 H2W 0.9061
57 F40 0.9059
58 91F 0.9057
59 3WN 0.9047
60 3WO 0.9047
61 ZIP 0.9047
62 LI7 0.9042
63 9F8 0.9042
64 HVE 0.9040
65 3B4 0.9039
66 FY8 0.9028
67 INI 0.9027
68 B4L 0.9021
69 MJW 0.9021
70 MUK 0.9016
71 4GU 0.9015
72 DE7 0.9012
73 3G1 0.9011
74 7VY 0.9006
75 NU3 0.9006
76 M01 0.9005
77 5ER 0.9005
78 AZC 0.9004
79 BZC 0.9004
80 3IP 0.9000
81 KTV 0.8996
82 4K2 0.8992
83 8UY 0.8983
84 UAY 0.8982
85 TCW 0.8977
86 55D 0.8975
87 U13 0.8975
88 4ZF 0.8975
89 GAT 0.8974
90 8M5 0.8971
91 697 0.8968
92 3WK 0.8964
93 9CE 0.8963
94 2KU 0.8962
95 TRF 0.8962
96 3M8 0.8959
97 AKD 0.8958
98 G1N 0.8957
99 U19 0.8953
100 CQW 0.8949
101 WA2 0.8947
102 KTM 0.8946
103 38E 0.8943
104 5NN 0.8943
105 RNK 0.8938
106 1Q4 0.8931
107 6DQ 0.8931
108 A64 0.8926
109 NAR 0.8924
110 O53 0.8915
111 ZYC 0.8913
112 1UT 0.8912
113 RE4 0.8911
114 1V0 0.8910
115 G30 0.8909
116 3GX 0.8907
117 5WW 0.8904
118 ELH 0.8901
119 ZEZ 0.8900
120 DXK 0.8900
121 ZRK 0.8899
122 SCE 0.8898
123 4A1 0.8890
124 GZV 0.8889
125 NX5 0.8888
126 QUB 0.8886
127 CFK 0.8886
128 AX5 0.8886
129 4L2 0.8884
130 3WJ 0.8881
131 C4E 0.8879
132 CJZ 0.8877
133 DL6 0.8874
134 P4L 0.8873
135 GAL PHB 0.8871
136 5VU 0.8869
137 1V4 0.8868
138 AGI 0.8858
139 L21 0.8858
140 FER 0.8857
141 1UR 0.8857
142 L12 0.8857
143 2QV 0.8853
144 7L4 0.8851
145 LLG 0.8850
146 GA2 0.8850
147 MH5 0.8848
148 FLF 0.8847
149 8BD 0.8846
150 EDZ 0.8846
151 244 0.8839
152 B2E 0.8838
153 NIY 0.8836
154 NIP 0.8836
155 25K 0.8835
156 GJK 0.8833
157 5YA 0.8832
158 JTY 0.8832
159 2LX 0.8828
160 AJD 0.8827
161 9JT 0.8824
162 B5A 0.8824
163 5WM 0.8823
164 78P 0.8821
165 WCU 0.8820
166 5TU 0.8820
167 P9I 0.8818
168 7NU 0.8818
169 M02 0.8815
170 GVI 0.8814
171 HA6 0.8814
172 HFT 0.8811
173 V15 0.8809
174 IKY 0.8805
175 NX1 0.8805
176 VXM 0.8802
177 1FL 0.8800
178 0SY 0.8799
179 1V3 0.8798
180 DFV 0.8797
181 NXY 0.8794
182 L3L 0.8791
183 LU2 0.8790
184 SGW 0.8789
185 NPZ 0.8786
186 VGG 0.8782
187 RB1 0.8781
188 CWE 0.8780
189 RK4 0.8777
190 2VQ 0.8775
191 LR2 0.8774
192 6T5 0.8770
193 PNJ 0.8769
194 6EN 0.8768
195 BDI 0.8764
196 1V8 0.8759
197 JF8 0.8757
198 A51 0.8757
199 AJ4 0.8756
200 NBZ GLA 0.8755
201 6TJ 0.8754
202 5CX 0.8750
203 6J3 0.8744
204 7W7 0.8742
205 56N 0.8740
206 EVO 0.8739
207 TQ3 0.8737
208 STL 0.8735
209 57D 0.8733
210 YEX 0.8732
211 6BK 0.8729
212 8HH 0.8728
213 2J5 0.8726
214 1VQ 0.8726
215 LMZ 0.8725
216 AP6 0.8723
217 A7K 0.8722
218 PE2 0.8717
219 E9S 0.8717
220 3D3 0.8716
221 CUH 0.8716
222 P4T 0.8715
223 CBE 0.8714
224 JNW 0.8714
225 ASE 0.8712
226 1BY 0.8710
227 3JC 0.8709
228 7WD 0.8709
229 BNY 0.8708
230 GJB 0.8707
231 PLP 0.8707
232 CU5 0.8703
233 5P3 0.8702
234 BBY 0.8698
235 2GQ 0.8697
236 2LT 0.8694
237 NE2 0.8694
238 ONZ 0.8693
239 IDD 0.8693
240 5CE 0.8687
241 TLF 0.8683
242 ID8 0.8681
243 LJ5 0.8668
244 2QU 0.8665
245 BJ4 0.8664
246 PNW 0.8663
247 0H5 0.8661
248 SNP 0.8659
249 OLN 0.8659
250 G6P 0.8658
251 4Y2 0.8658
252 147 0.8658
253 8KW 0.8655
254 4MX 0.8653
255 53X 0.8651
256 FF2 0.8648
257 Q9T 0.8647
258 AQ1 0.8646
259 AC2 0.8643
260 P2L 0.8641
261 LQG 0.8637
262 C9M 0.8635
263 SXX 0.8634
264 7ZL 0.8632
265 IK1 0.8629
266 GI2 0.8629
267 26C 0.8628
268 PXP 0.8627
269 X8E 0.8624
270 5S9 0.8621
271 LJ2 0.8620
272 JZR 0.8620
273 R4E 0.8619
274 HWH 0.8619
275 IAG 0.8618
276 28A 0.8618
277 IEE 0.8614
278 IMK 0.8613
279 4JV 0.8603
280 LJ1 0.8603
281 AXX 0.8602
282 5E1 0.8600
283 ZYV 0.8596
284 CUQ 0.8593
285 5B2 0.8589
286 41L 0.8586
287 RGG 0.8578
288 SNY 0.8578
289 536 0.8575
290 3Y7 0.8571
291 7ZO 0.8565
292 3CA 0.8556
293 P2C 0.8554
294 ZMG 0.8541
295 KHP 0.8539
296 BVB 0.8535
297 OA4 0.8528
298 IW6 0.8527
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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