Receptor
PDB id Resolution Class Description Source Keywords
5WBO 2.25 Å EC: 2.7.1.3 STRUCTURE OF HUMAN KETOHEXOKINASE COMPLEXED WITH HITS FROM F SCREENING HOMO SAPIENS KETOHEXOKINASE FRAGMENT-BASED DRUG DISCOVERY SBDD TRANSFE
Ref.: DISCOVERY OF FRAGMENT-DERIVED SMALL MOLECULES FOR I INHIBITION OF KETOHEXOKINASE (KHK). J. MED. CHEM. V. 60 7835 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CIT A:303;
B:304;
 Invalid;
Invalid;
 none;
none;
 submit data
192.124 C6 H8 O7 C(C(=...
A1Y B:301;
A:301;
 Valid;
Valid;
 none;
none;
 Kd = 62 uM
217.267 C12 H15 N3 O Cc1cc...
SO4 A:302;
B:303;
B:302;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
96.063 O4 S [O-]S...
GOL B:305;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6W0Z 2.3 Å EC: 2.7.1.3 STRUCTURE OF KHK IN COMPLEX WITH COMPOUND 8 (2-[(1~{S},5~{R} [(2~{S})-2-METHYLAZETIDIN-1-YL]-6-(TRIFLUOROMETHYL)PYRIMIDIA ZABICYCLO[3.1.0]HEXAN-6-YL]ETHANOIC ACID) HOMO SAPIENS KETOHEXOKINASE TRANSFERASE
Ref.: DISCOVERY OF PF-06835919: A POTENT INHIBITOR OF KETOHEXOKINASE (KHK) FOR THE TREATMENT OF METABOLIC DISORDERS DRIVEN BY THE OVERCONSUMPTION OF FRUCTOSE J.MED.CHEM. V. 63 13546 2020
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6W0Z ic50 = 0.01 uM S6D C16 H19 F3 N4 O2 C[C@H]1CCN....
2 3NBW - TR4 C11 H10 N4 S CSc1c(c(n(....
3 5WBM Kd = 20 uM A4G C13 H18 N4 O Cc1c[nH]c2....
4 5WBO Kd = 62 uM A1Y C12 H15 N3 O Cc1cc(nc(c....
5 6W0X ic50 = 0.14 uM S6J C17 H19 F3 N4 O2 C[C@H]1[C@....
6 5WBQ ic50 = 1.48 uM A3J C16 H17 F3 N4 O CCc1cc2c([....
7 6W0N ic50 = 0.41 uM RYS C16 H19 F3 N4 O3 C[C@@]1(CC....
8 3NBV - FRU C6 H12 O6 C([C@@H]1[....
9 5WBZ ic50 = 0.39 uM A4J C16 H19 F3 N4 O3 C[C@@]1(CC....
10 3NC2 - QUZ C8 H6 N2 c1ccc2c(c1....
11 3NC9 ic50 = 330 nM TR3 C20 H22 N4 O S CSc1c2ccc(....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6W0Z ic50 = 0.01 uM S6D C16 H19 F3 N4 O2 C[C@H]1CCN....
2 3NBW - TR4 C11 H10 N4 S CSc1c(c(n(....
3 5WBM Kd = 20 uM A4G C13 H18 N4 O Cc1c[nH]c2....
4 5WBO Kd = 62 uM A1Y C12 H15 N3 O Cc1cc(nc(c....
5 6W0X ic50 = 0.14 uM S6J C17 H19 F3 N4 O2 C[C@H]1[C@....
6 5WBQ ic50 = 1.48 uM A3J C16 H17 F3 N4 O CCc1cc2c([....
7 6W0N ic50 = 0.41 uM RYS C16 H19 F3 N4 O3 C[C@@]1(CC....
8 3NBV - FRU C6 H12 O6 C([C@@H]1[....
9 5WBZ ic50 = 0.39 uM A4J C16 H19 F3 N4 O3 C[C@@]1(CC....
10 3NC2 - QUZ C8 H6 N2 c1ccc2c(c1....
11 3NC9 ic50 = 330 nM TR3 C20 H22 N4 O S CSc1c2ccc(....
12 2HW1 - FRU C6 H12 O6 C([C@@H]1[....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6W0Z ic50 = 0.01 uM S6D C16 H19 F3 N4 O2 C[C@H]1CCN....
2 3NBW - TR4 C11 H10 N4 S CSc1c(c(n(....
3 5WBM Kd = 20 uM A4G C13 H18 N4 O Cc1c[nH]c2....
4 5WBO Kd = 62 uM A1Y C12 H15 N3 O Cc1cc(nc(c....
5 6W0X ic50 = 0.14 uM S6J C17 H19 F3 N4 O2 C[C@H]1[C@....
6 5WBQ ic50 = 1.48 uM A3J C16 H17 F3 N4 O CCc1cc2c([....
7 6W0N ic50 = 0.41 uM RYS C16 H19 F3 N4 O3 C[C@@]1(CC....
8 3NBV - FRU C6 H12 O6 C([C@@H]1[....
9 5WBZ ic50 = 0.39 uM A4J C16 H19 F3 N4 O3 C[C@@]1(CC....
10 3NC2 - QUZ C8 H6 N2 c1ccc2c(c1....
11 3NC9 ic50 = 330 nM TR3 C20 H22 N4 O S CSc1c2ccc(....
12 2HW1 - FRU C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: A1Y; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 A1Y 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: A1Y; Similar ligands found: 316
No: Ligand Similarity coefficient
1 B4O 0.9514
2 M4B 0.9489
3 49O 0.9406
4 BPY 0.9382
5 977 0.9341
6 QZ8 0.9333
7 JUO 0.9332
8 SYR 0.9252
9 N3W 0.9236
10 22L 0.9220
11 8WZ 0.9216
12 3Y7 0.9196
13 MIL 0.9188
14 TQU 0.9182
15 JR2 0.9180
16 AM1 0.9180
17 BQ5 0.9162
18 BCK 0.9148
19 89J 0.9146
20 MPK 0.9145
21 2JK 0.9142
22 CMU 0.9118
23 96U 0.9114
24 W8G 0.9109
25 MOK 0.9103
26 6J9 0.9090
27 1FF 0.9087
28 A9O 0.9078
29 49N 0.9077
30 H70 0.9077
31 NQH 0.9072
32 K3Y 0.9066
33 F69 0.9065
34 BPS 0.9064
35 G1P 0.9060
36 1WC 0.9057
37 BZE 0.9056
38 2LX 0.9052
39 PBQ 0.9048
40 JRB 0.9037
41 CP6 0.9032
42 4KL 0.9031
43 K25 0.9030
44 ONR 0.9028
45 AY4 0.9023
46 M3E 0.9015
47 5V7 0.9014
48 25O 0.9013
49 B2Y 0.9013
50 SV4 0.9009
51 NBG 0.9002
52 CG8 0.8994
53 52C 0.8993
54 96R 0.8989
55 8GK 0.8986
56 CR1 0.8985
57 HPT 0.8984
58 CCV 0.8979
59 GF4 0.8977
60 T6Z 0.8976
61 ZYW 0.8975
62 YO5 0.8964
63 NPL 0.8964
64 DNC 0.8959
65 5WU 0.8953
66 XDK 0.8953
67 MUR 0.8952
68 OBP 0.8950
69 WOE 0.8949
70 0F9 0.8946
71 6XI 0.8944
72 IBM 0.8943
73 60Q 0.8940
74 S3C 0.8935
75 GI3 0.8929
76 5JT 0.8927
77 SQ4 0.8925
78 8G6 0.8924
79 A9P 0.8924
80 CPW 0.8924
81 CGW 0.8916
82 N2Z 0.8916
83 MXD 0.8914
84 CLU 0.8909
85 K44 0.8908
86 9GP 0.8907
87 DNB 0.8906
88 7I2 0.8905
89 4GP 0.8899
90 DNA 0.8898
91 4MX 0.8893
92 KP2 0.8892
93 DK1 0.8890
94 XFE 0.8889
95 XM5 0.8888
96 BY5 0.8886
97 G6P 0.8884
98 BG6 0.8883
99 30G 0.8882
100 PVQ 0.8882
101 PVK 0.8876
102 OUB 0.8876
103 NAG 0.8875
104 XQK 0.8873
105 3B4 0.8873
106 SBK 0.8872
107 1XA 0.8868
108 OX2 0.8868
109 HJ8 0.8866
110 LT8 0.8864
111 UFO 0.8863
112 AMQ 0.8862
113 AMR 0.8862
114 NCV 0.8857
115 S7B 0.8855
116 4R1 0.8854
117 56N 0.8852
118 H5B 0.8852
119 5NS 0.8850
120 9X5 0.8846
121 GI1 0.8845
122 A4G 0.8845
123 SQ7 0.8844
124 1A7 0.8843
125 W29 0.8839
126 IPT 0.8837
127 HA5 0.8831
128 IA2 0.8831
129 5E4 0.8826
130 TR4 0.8825
131 6HP 0.8825
132 F5C 0.8822
133 LJ3 0.8821
134 PLP 0.8820
135 1X8 0.8814
136 54X 0.8814
137 M6P 0.8814
138 3DT 0.8813
139 1QV 0.8812
140 ESI 0.8811
141 DHZ 0.8809
142 UAN 0.8804
143 DBQ 0.8803
144 3J8 0.8800
145 5VJ 0.8800
146 B2T 0.8798
147 512 0.8792
148 TNF 0.8789
149 7WR 0.8788
150 CE2 0.8788
151 NBV 0.8787
152 IBC 0.8784
153 KFN 0.8784
154 GRX 0.8781
155 X11 0.8781
156 APS 0.8781
157 K3Q 0.8781
158 97T 0.8781
159 JP2 0.8778
160 CH9 0.8777
161 344 0.8777
162 4ME 0.8776
163 Z5P 0.8772
164 HQD 0.8772
165 LIP 0.8771
166 C93 0.8769
167 8XQ 0.8767
168 AJD 0.8766
169 DXK 0.8765
170 PMP 0.8764
171 I6G 0.8764
172 5P3 0.8764
173 9UL 0.8758
174 505 0.8757
175 QMS 0.8755
176 PRZ 0.8755
177 KED 0.8751
178 M1Z 0.8751
179 KF5 0.8749
180 C9E 0.8745
181 AKD 0.8740
182 8MO 0.8736
183 2GQ 0.8736
184 7MX 0.8733
185 9AP 0.8732
186 209 0.8729
187 CKA 0.8729
188 AC2 0.8728
189 BGU 0.8727
190 CC5 0.8727
191 GDE 0.8726
192 SG2 0.8726
193 LDR 0.8723
194 6DP 0.8721
195 GAT 0.8720
196 ZYR 0.8710
197 6TZ 0.8709
198 FWD 0.8708
199 67Y 0.8706
200 7ZL 0.8706
201 ARP 0.8704
202 ANC 0.8700
203 B23 0.8700
204 K37 0.8696
205 KYA 0.8696
206 URI 0.8696
207 VXX 0.8696
208 HMD 0.8694
209 I59 0.8694
210 NDG 0.8693
211 2KU 0.8692
212 THM 0.8691
213 Q0K 0.8690
214 B56 0.8689
215 M3Q 0.8689
216 PXP 0.8688
217 6QF 0.8686
218 STT 0.8686
219 K48 0.8685
220 CTN 0.8685
221 THA 0.8685
222 FLV 0.8683
223 EYA 0.8677
224 S2T 0.8676
225 68A 0.8675
226 TWO 0.8673
227 5OF 0.8672
228 8NX 0.8672
229 4XS 0.8670
230 EYM 0.8669
231 KTW 0.8669
232 J9Q 0.8668
233 GN6 0.8664
234 3RI 0.8662
235 6J3 0.8661
236 4XY 0.8661
237 N7I 0.8661
238 FTV 0.8660
239 GZ2 0.8659
240 537 0.8658
241 2K8 0.8658
242 8D6 0.8657
243 RME 0.8657
244 878 0.8655
245 ABJ 0.8650
246 4NR 0.8649
247 EXR 0.8648
248 IPD 0.8648
249 MUK 0.8647
250 8W9 0.8647
251 FNA 0.8647
252 HQJ 0.8642
253 FDR 0.8640
254 PIR 0.8640
255 293 0.8639
256 5F8 0.8637
257 RB2 0.8637
258 RUG 0.8637
259 5GL 0.8636
260 2F6 0.8635
261 9F8 0.8632
262 X48 0.8630
263 5FL 0.8629
264 9PL 0.8628
265 GNG 0.8621
266 M6D 0.8620
267 50C 0.8619
268 BP7 0.8619
269 JG8 0.8618
270 P9I 0.8617
271 F01 0.8617
272 ID2 0.8616
273 FMQ 0.8614
274 2FQ 0.8614
275 IQW 0.8611
276 8HC 0.8611
277 H33 0.8610
278 RUY 0.8610
279 5AD 0.8609
280 MCY 0.8606
281 LP8 0.8605
282 EXD 0.8605
283 V1T 0.8605
284 0FK 0.8605
285 JF2 0.8604
286 0DN 0.8588
287 2GD 0.8585
288 774 0.8585
289 R20 0.8584
290 X04 0.8584
291 F6P 0.8582
292 JF1 0.8582
293 DPT 0.8580
294 B86 0.8579
295 H4B 0.8579
296 5BT 0.8571
297 APZ 0.8570
298 XZ8 0.8567
299 226 0.8564
300 QNA 0.8558
301 4XV 0.8557
302 11G 0.8553
303 PW1 0.8551
304 AA 0.8550
305 5WT 0.8550
306 GC2 0.8548
307 TIY 0.8548
308 B21 0.8544
309 HHS 0.8541
310 WS7 0.8539
311 772 0.8538
312 ZYQ 0.8538
313 2AN 0.8536
314 2FD 0.8533
315 KOM 0.8530
316 XQI 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6W0Z; Ligand: S6D; 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: 6w0z.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6W0Z; Ligand: S6D; 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: 6w0z.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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