Receptor
PDB id Resolution Class Description Source Keywords
2A2X 2.44 Å EC: 3.4.21.5 ORALLY ACTIVE THROMBIN INHIBITORS IN COMPLEX WITH THROMBIN I HOMO SAPIENS BLOOD CLOTTING SERINE PROTEASE HYDROLASE-HYDROLASE INHIBITCOMPLEX
Ref.: ORALLY ACTIVE THROMBIN INHIBITORS. PART 2: OPTIMIZA THE P2-MOIETY BIOORG.MED.CHEM.LETT. V. 16 2648 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA9 H:501;
Valid;
none;
ic50 = 20.2 nM
446.543 C22 H34 N6 O4 [H]/N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2A2X 2.44 Å EC: 3.4.21.5 ORALLY ACTIVE THROMBIN INHIBITORS IN COMPLEX WITH THROMBIN I HOMO SAPIENS BLOOD CLOTTING SERINE PROTEASE HYDROLASE-HYDROLASE INHIBITCOMPLEX
Ref.: ORALLY ACTIVE THROMBIN INHIBITORS. PART 2: OPTIMIZA THE P2-MOIETY BIOORG.MED.CHEM.LETT. V. 16 2648 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 2A2X ic50 = 20.2 nM NA9 C22 H34 N6 O4 [H]/N=C(c1....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 2A2X ic50 = 20.2 nM NA9 C22 H34 N6 O4 [H]/N=C(c1....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 2A2X ic50 = 20.2 nM NA9 C22 H34 N6 O4 [H]/N=C(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NA9; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 NA9 1 1
2 N12 0.578431 0.793651
3 CDO 0.542056 0.828125
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2A2X; Ligand: NA9; Similar sites found: 302
This union binding pocket(no: 1) in the query (biounit: 2a2x.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F4S EFO 0.001807 0.43198 None
2 3ZZS TRP 0.00195 0.42094 None
3 3SHR CMP 0.0003115 0.45063 0.772201
4 1ZK4 NAP 0.006229 0.43155 1.19522
5 1ZK4 AC0 0.006229 0.43155 1.19522
6 1G8S MET 0.00009556 0.50123 1.30435
7 1NJR XYL 0.0009138 0.42323 1.5444
8 2Q1W NAD 0.001352 0.42292 1.5444
9 3ZV6 4HB 0.001875 0.42928 1.9305
10 3ZV6 NAD 0.001761 0.42928 1.9305
11 3FC4 EDO 0.007167 0.41569 1.9305
12 1GV0 NAD 0.003349 0.40606 1.9305
13 3GWT 066 0.004149 0.40404 1.9305
14 1PR9 NAP 0.006158 0.40032 2.04918
15 4FR3 LYS ARG ARG LYS SEP VAL 0.02975 0.40004 2.13675
16 3MAG 3MA 0.008844 0.44184 2.3166
17 4NTD FAD 0.0009256 0.43641 2.3166
18 4KQI NIO 0.0007847 0.43005 2.3166
19 4KQI RBZ 0.0007847 0.43005 2.3166
20 4E13 NAD 0.0003707 0.42608 2.3166
21 1X1T NAD 0.008533 0.42261 2.3166
22 3NKS FAD 0.003074 0.41598 2.3166
23 1G41 ADP 0.009059 0.41246 2.3166
24 1ZFJ IMP 0.02708 0.41171 2.3166
25 1LDM NAD 0.01368 0.41076 2.3166
26 9LDT NAD 0.003697 0.40585 2.3166
27 3E8N VRA 0.008113 0.40529 2.3166
28 3E8N ATP 0.008113 0.40529 2.3166
29 1D3V ABH 0.002549 0.40442 2.3166
30 3H9E NAD 0.003234 0.40232 2.3166
31 3MCT SAH 0.002027 0.40097 2.3166
32 9LDB NAD 0.00523 0.40042 2.3166
33 2F3R G5P 0.003417 0.42406 2.41546
34 1DR1 NAP 0.002316 0.42052 2.6455
35 1DR1 HBI 0.002316 0.42052 2.6455
36 3R35 4CO 0.002019 0.4153 2.64901
37 1V6A TRE 0.001601 0.44031 2.7027
38 1K6M AGS 0.0008616 0.41555 2.7027
39 1I0Z NAI 0.002828 0.40869 2.7027
40 2WUF KEM 0.001789 0.40644 2.7027
41 4GYW UDP 0.00435 0.40458 2.7027
42 3V91 UPG 0.001987 0.40311 2.7027
43 3RO7 TDR 0.003466 0.40274 2.7027
44 1S8F GDP 0.002132 0.4087 2.82486
45 2RDT 2RD 0.006236 0.42567 3.0888
46 3TO7 COA 0.002979 0.41758 3.0888
47 2B4Q NAP 0.001752 0.41613 3.0888
48 3RFV NAI 0.001819 0.41265 3.0888
49 1DLJ UGA 0.008816 0.40989 3.0888
50 3CKJ CIT 0.002116 0.40881 3.0888
51 1DLJ NAI 0.009398 0.40881 3.0888
52 1H6C SIN 0.007276 0.40418 3.0888
53 2C31 ADP 0.02517 0.40355 3.0888
54 2C31 TZD 0.02595 0.40355 3.0888
55 4JEJ 1GP 0.0000628 0.42404 3.27869
56 2Q37 3AL 0.004715 0.42022 3.31492
57 1Y13 BIO 0.0001017 0.41318 3.31492
58 1MVN PCO 0.01459 0.40541 3.34928
59 1I52 CTP 0.004192 0.40257 3.38983
60 4L1F FAD 0.000594 0.43854 3.4749
61 2DTX BMA 0.002888 0.41915 3.4749
62 1LVL FAD 0.003759 0.41885 3.4749
63 2R5T ANP 0.0007479 0.41571 3.4749
64 1OAA OAA 0.00602 0.41111 3.4749
65 1A5Z NAD 0.01026 0.40575 3.4749
66 1LVL NAD 0.001955 0.40151 3.4749
67 4NAT 2W5 0.007149 0.40241 3.75
68 3F81 STT 0.002686 0.45963 3.82514
69 3F3E LEU 0.001393 0.42868 3.861
70 2J7T 274 0.001943 0.41311 3.861
71 3FC2 IBI 0.002135 0.41306 3.861
72 1SB8 UD2 0.01114 0.40748 3.861
73 3ZEI AWH 0.002993 0.40643 3.861
74 4KOA NDP 0.0007569 0.40628 3.861
75 1SB8 NAD 0.0144 0.40007 3.861
76 1UXG NAD 0.0007478 0.43984 4.2471
77 1UXG FUM 0.0007478 0.43984 4.2471
78 2Q1S NAI 0.001203 0.43755 4.2471
79 1FL2 FAD 0.001472 0.43114 4.2471
80 4NM5 ADP 0.0004167 0.42636 4.2471
81 3FPZ AHZ 0.00893 0.42515 4.2471
82 2NVK FAD 0.002574 0.42309 4.2471
83 3PVT 3HC 0.004227 0.41086 4.2471
84 2Q2V NAD 0.001506 0.42254 4.31373
85 1YOA FAD 0.0004019 0.4269 4.40252
86 4COQ SAN 0.012 0.40809 4.45344
87 4BAS GNP 0.0003742 0.42595 4.52261
88 1TIW FAD 0.0008169 0.43842 4.6332
89 1TIW TFB 0.0008169 0.43842 4.6332
90 1CSI OAA 0.002936 0.41888 4.6332
91 1CSI CMX 0.002936 0.41888 4.6332
92 3BW2 FMN 0.002288 0.41199 4.6332
93 1REO FAD 0.005526 0.40864 4.6332
94 1B8U OAA 0.003977 0.40598 4.6332
95 1PL6 572 0.004441 0.40548 4.6332
96 4HA6 FAD 0.008827 0.40481 4.6332
97 2DKH 3HB 0.00783 0.40299 4.6332
98 1H2B NAJ 0.005611 0.40179 4.6332
99 1I9G SAM 0.01199 0.40149 4.6332
100 2YVF FAD 0.005963 0.42315 5.01931
101 2YVF NAD 0.006203 0.42315 5.01931
102 3DAG FEG 0.0007527 0.42294 5.01931
103 2Z9V PXM 0.005168 0.41308 5.01931
104 3K3K A8S 0.001874 0.40021 5.21327
105 1U7Z PMT 0.002778 0.41288 5.30973
106 1V7R CIT 0.001499 0.48213 5.37634
107 1H82 FAD 0.002852 0.4336 5.40541
108 1H82 GZZ 0.008044 0.418 5.40541
109 1XVV CCQ 0.00522 0.40956 5.40541
110 3LM9 FRU 0.001833 0.40778 5.40541
111 3M31 FAD 0.001644 0.40771 5.40541
112 4EPM AMP 0.002376 0.40219 5.40541
113 1GS5 NLG 0.005584 0.40186 5.42636
114 1GS5 ANP 0.005584 0.40186 5.42636
115 2F01 BTQ 0.01555 0.40915 5.51181
116 2F01 BTN 0.01638 0.40824 5.51181
117 1HFS L04 0.0007945 0.43126 5.625
118 1Y42 TYR 0.001687 0.43321 5.79151
119 1SOW NAD 0.0009562 0.42835 5.79151
120 2G86 UMP 0.006774 0.4135 5.79151
121 2NP9 YE1 0.003559 0.40773 5.79151
122 1RM4 NDP 0.003189 0.40254 5.79151
123 1SS4 GSH 0.0005027 0.52822 5.88235
124 1SS4 CIT 0.04059 0.44483 5.88235
125 1O6B ADP 0.01073 0.40247 5.91716
126 3S9K CIT 0.00562 0.45966 5.9322
127 2OD9 A1R NCA 0.000568 0.43362 6.17761
128 1XHL NDP 0.001514 0.42115 6.17761
129 3NYQ AMP 0.001769 0.42001 6.17761
130 3NYQ MCA 0.001743 0.41893 6.17761
131 2QQF A1R 0.001371 0.41384 6.17761
132 1DSS NAD 0.001445 0.41303 6.17761
133 4O1M NAD 0.004879 0.40021 6.17761
134 2FWP ICR 0.006427 0.40195 6.55738
135 4B4D FAD 0.001548 0.40496 6.56371
136 3TN7 NJP 0.002256 0.41357 6.61479
137 4LWM MHO 0.03853 0.40864 6.91244
138 1T26 NAI 0.008053 0.43296 6.94981
139 1T26 GBD 0.008053 0.43296 6.94981
140 2YPO PHE 0.001978 0.41425 6.94981
141 2JBZ COA 0.01251 0.4012 6.99301
142 3ZY6 GFB 0.001471 0.40571 7.33591
143 4IEN COA 0.002132 0.41769 7.36196
144 2GYI HYA 0.01634 0.40768 7.72201
145 2BJK NAD 0.01179 0.40689 7.72201
146 1HPG BOC ALA ALA PRO GLU 0.0007056 0.42141 8.02139
147 1C1L GAL BGC 0.006067 0.42752 8.0292
148 2NCD ADP 0.002044 0.43576 8.10811
149 2A0W DIH 0.003816 0.40848 8.10811
150 3ZPG 5GP 0.0009716 0.48168 8.49421
151 1V35 NAI 0.003888 0.41636 8.49421
152 2AQJ TRP 0.002961 0.43371 8.82353
153 2AQJ FAD 0.003091 0.43371 8.82353
154 1R6D NAD 0.003164 0.42952 8.82353
155 1RHC F42 ACN 0.0008659 0.42708 8.82353
156 4DEM YS4 0.009741 0.42465 8.82353
157 2NT8 ATP 0.001023 0.42301 8.82353
158 3T31 DCQ 0.007123 0.418 8.82353
159 3T31 FAD 0.006537 0.418 8.82353
160 2V7T SAH 0.02217 0.41276 8.82353
161 4NE2 SH2 0.00437 0.40809 8.82353
162 1R6D DAU 0.01178 0.40654 8.82353
163 1XOC VAL ASP SER LYS ASN THR SER SER TRP 0.007283 0.40516 8.82353
164 1YBH FAD 0.03553 0.40328 8.82353
165 3HAZ NAD 0.004032 0.40317 8.82353
166 1RYI FAD 0.01005 0.40268 8.82353
167 4NE2 ADP 0.005895 0.40218 8.82353
168 1KBI PYR 0.003402 0.40155 8.82353
169 1KBI FMN 0.003402 0.40155 8.82353
170 1RYI GOA 0.01113 0.40099 8.82353
171 4SGA ACE PRO ALA PRO PHE 0.0001228 0.45738 8.83978
172 4P53 NAI 0.0003885 0.43636 8.88031
173 2AMV BIN 0.008041 0.41143 8.88031
174 4F8L GAL 0.01346 0.44096 8.96552
175 2C9O ADP 0.002087 0.41611 9.26641
176 1JYQ MAZ PTR PTM ASN 0.002649 0.43003 9.375
177 2OUA AES 0.00001589 0.40846 9.57447
178 1NNU NAD 0.01141 0.42183 10
179 1NNU TCT 0.03211 0.40326 10
180 3U4C NDP 0.003354 0.40466 10.0386
181 2V6O FAD 0.0009086 0.46315 10.8108
182 2HV8 GTP 0.000694 0.42244 10.9375
183 4GQB 0XU 0.004103 0.42434 11.583
184 4R33 SAH 0.0002041 0.45403 11.7647
185 4R33 TRP 0.0002041 0.45403 11.7647
186 1C0I FAD 0.0006333 0.45013 11.7647
187 1C0I BE2 0.0006333 0.45013 11.7647
188 1IYE PGU 0.0004164 0.43994 11.7647
189 3RSR N5P 0.002673 0.41933 11.7647
190 2JL1 NAP 0.001309 0.40932 11.7647
191 4KCF AKM 0.001673 0.40745 11.7647
192 3AXB PRO 0.007885 0.40576 11.7647
193 3AXB FAD 0.005807 0.40576 11.7647
194 3DDC GNP 0.002802 0.40297 11.7647
195 2ALG DAO 0.001597 0.40449 11.9565
196 2ALG HP6 0.001597 0.40449 11.9565
197 2C7G FAD 0.003342 0.43014 12.3552
198 2C7G ODP 0.003194 0.43014 12.3552
199 2FH5 GTP 0.001056 0.40861 12.4324
200 1YB5 NAP 0.004343 0.40703 13.1274
201 2GJ3 FAD 0.02878 0.40326 13.3333
202 1D6H COA 0.001157 0.4382 13.5135
203 1H9A NAP 0.003319 0.41129 13.5135
204 1ZK7 FAD 0.0002841 0.46337 14.7059
205 4FWE FAD 0.0005332 0.4509 14.7059
206 1TDF FAD 0.00126 0.43973 14.7059
207 1TDF NAP 0.004306 0.4346 14.7059
208 2RGH FAD 0.002665 0.4215 14.7059
209 4G87 UD1 0.00485 0.41693 14.7059
210 1RKD RIB 0.002032 0.41653 14.7059
211 1RKD ADP 0.002032 0.41653 14.7059
212 1RLZ NAD 0.01485 0.41055 14.7059
213 4KQL 1SG 0.01339 0.40988 14.7059
214 2XD9 XD9 0.01387 0.43522 15.5689
215 2E1A MSE 0.00131 0.43191 16
216 1GR0 NAD 0.002087 0.44854 17.6471
217 4AT0 FAD 0.002986 0.42631 17.6471
218 3Q9T FAY 0.002046 0.42363 17.6471
219 1P9B IMO 0.0008067 0.42017 17.6471
220 1LTH NAD 0.005623 0.41902 17.6471
221 2QA1 FAD 0.002889 0.41469 17.6471
222 1ME8 RVP 0.01788 0.41279 17.6471
223 1HV9 UD1 0.002742 0.41182 17.6471
224 2YB9 HA0 0.002654 0.40968 17.6471
225 2HGS ADP 0.002086 0.40238 17.6471
226 4Q3R XA2 0.002936 0.40227 17.6471
227 1PEA ACM 0.005451 0.43661 18.9189
228 3LZW NAP 0.001931 0.441 20.5882
229 3WE0 FAD 0.001051 0.43977 20.5882
230 1Q3Q ANP 0.002799 0.43238 20.5882
231 3LZW FAD 0.001293 0.43102 20.5882
232 1RBO CAP 0.01675 0.42863 20.5882
233 1EP2 FMN 0.001023 0.42149 20.5882
234 1VDC FAD 0.004015 0.42138 20.5882
235 3ICC NAP 0.00259 0.41272 20.5882
236 4KGD FAD 0.01465 0.41254 20.5882
237 4KGD TDP 0.01418 0.41254 20.5882
238 1EP2 ORO 0.004305 0.40717 20.5882
239 2OYS FMN 0.001398 0.40646 20.5882
240 1M7Y PPG 0.003391 0.40587 20.5882
241 1T57 FMN 0.001819 0.40442 20.5882
242 3FSJ D7K 0.02833 0.40036 20.5882
243 4A3R CIT 0.005318 0.40497 21.2355
244 4B63 ORN 0.007443 0.44634 23.5294
245 4B63 NAP 0.007716 0.44634 23.5294
246 4B63 FAD 0.007443 0.44634 23.5294
247 3GE7 AFQ 0.0005998 0.43705 23.5294
248 2YHW BM3 0.0006567 0.43137 23.5294
249 1E8G FAD 0.01192 0.42583 23.5294
250 1E8G FCR 0.01622 0.41934 23.5294
251 1M5B BN1 0.007283 0.41762 23.5294
252 1OYB HBA 0.001909 0.41038 23.5294
253 1OYB FMN 0.001376 0.41038 23.5294
254 1I2B UPG 0.0118 0.40798 23.5294
255 1I2B NAD 0.0118 0.40798 23.5294
256 1I2B USQ 0.0118 0.40798 23.5294
257 2WQP WQP 0.002589 0.40573 23.5294
258 1NVU GTP 0.01387 0.40522 23.5294
259 3Q3C NAD 0.01297 0.4049 23.5294
260 2EJU SAH 0.001643 0.4001 23.5294
261 4PLG NAI 0.0008645 0.43633 26.4706
262 4PLG OXM 0.0008645 0.43633 26.4706
263 2QQ0 ANP 0.0016 0.41893 26.4706
264 4IZC 1GZ 0.007108 0.4131 26.4706
265 2QQ0 ADP 0.002462 0.4122 26.4706
266 2QQ0 TMP 0.002462 0.4122 26.4706
267 2QQ0 THM 0.004027 0.40184 26.4706
268 1BGQ RDC 0.0001818 0.44629 29.4118
269 1WDA BAG 0.0006082 0.44525 29.4118
270 4BMO FMN 0.001153 0.41647 29.4118
271 2XVF FAD 0.004633 0.40939 29.4118
272 2XVE FAD 0.01472 0.40824 29.4118
273 2RHQ GAX 0.0003179 0.40709 29.4118
274 1RP0 AHZ 0.0217 0.40506 29.4118
275 1FIQ FAD 0.0003771 0.44574 32.3529
276 4BJZ P3A 0.01121 0.41782 32.3529
277 4BJZ FAD 0.01121 0.41782 32.3529
278 3WBF NAP 0.001528 0.41682 32.3529
279 1FIQ SAL 0.003302 0.40891 32.3529
280 3WBF API 0.004038 0.40698 32.3529
281 1R27 MGD 0.005581 0.40531 32.3529
282 1FIQ MTE 0.004018 0.40323 32.3529
283 3KMZ EQO 0.003673 0.40038 32.3529
284 3EAU PDN 0.01756 0.4131 35.2941
285 3EAU NDP 0.01756 0.4131 35.2941
286 4CS4 ANP 0.0042 0.41096 35.2941
287 4CS4 AXZ 0.006586 0.40963 35.2941
288 2J07 HDF 0.01402 0.40131 35.2941
289 2J07 FAD 0.01402 0.40131 35.2941
290 3SSO SAH 0.001108 0.4099 41.1765
291 1EDO NAP 0.01754 0.4088 41.1765
292 3DCM SAM 0.0003074 0.42672 44.1176
293 1GJC 130 0.0000000005471 0.7341 45.0593
294 2GSD NAD 0.003602 0.41117 47.0588
295 1OSS BEN 0.00000000003267 0.6353 47.0852
296 1RTF BEN 0.000000000001797 0.65022 48.0159
297 3N7O N7O 0.0000005785 0.59141 48.6726
298 2AIQ BEN 0.00000001881 0.54978 48.9177
299 1FIW PBZ 0.00000000007826 0.66027 49.0347
300 1IAU ACE ILE GLU PRO ASJ 0.000000553 0.55594 49.3392
301 1PQ7 ARG 0.0000000007148 0.6715 49.5536
302 4NFE BEN 0.00000001295 0.54056 49.789
303 1AL8 DHP 0.01491 0.40927 50
Pocket No.: 2; Query (leader) PDB : 2A2X; Ligand: NA9; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 2a2x.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4YLU R30 0.004525 0.40413 3.4749
2 4YOI 4F4 0.006138 0.40261 8.49421
3 3DLG GWE 0.03531 0.40693 11.9691
4 5GUD NDP 0.02381 0.40103 12.7413
5 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.001179 0.44623 17.6471
6 5A8Y VBM 0.0000008865 0.56747 45.8716
7 1SQA UI1 0.0000000009688 0.73291 47.3469
Feedback