Receptor
PDB id Resolution Class Description Source Keywords
1O0D 2.44 Å EC: 3.4.21.5 HUMAN THROMBIN COMPLEXED WITH A D-PHE-PRO-ARG-TYPE INHIBITOR TERMINAL HIRUDIN DERIVED EXO-SITE INHIBITOR HOMO SAPIENS TERNARY COMPLEX; THROMBIN-ACTIVE-SITE INHIBITOR-EXO-SITE INHBLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX
Ref.: D-PHE-PRO-ARG TYPE THROMBIN INHIBITORS: UNEXPECTED SELECTIVITY BY MODIFICATION OF THE P1 MOIETY BIOORG.MED.CHEM.LETT. V. 13 2029 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
163 H:248;
Valid;
none;
ic50 = 6.2 nM
456.538 C23 H32 N6 O4 Cn1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1O0D 2.44 Å EC: 3.4.21.5 HUMAN THROMBIN COMPLEXED WITH A D-PHE-PRO-ARG-TYPE INHIBITOR TERMINAL HIRUDIN DERIVED EXO-SITE INHIBITOR HOMO SAPIENS TERNARY COMPLEX; THROMBIN-ACTIVE-SITE INHIBITOR-EXO-SITE INHBLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX
Ref.: D-PHE-PRO-ARG TYPE THROMBIN INHIBITORS: UNEXPECTED SELECTIVITY BY MODIFICATION OF THE P1 MOIETY BIOORG.MED.CHEM.LETT. V. 13 2029 2003
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 1O0D ic50 = 6.2 nM 163 C23 H32 N6 O4 Cn1c(ccc1C....
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 1O0D ic50 = 6.2 nM 163 C23 H32 N6 O4 Cn1c(ccc1C....
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 1O0D ic50 = 6.2 nM 163 C23 H32 N6 O4 Cn1c(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 163; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 163 1 1
2 162 0.704082 0.953125
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1O0D; Ligand: 163; Similar sites found: 23
This union binding pocket(no: 1) in the query (biounit: 1o0d.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2POC UD1 0.01378 0.40745 2.7027
2 4YLU R30 0.005735 0.40543 3.4749
3 3NOJ PYR 0.005224 0.44693 5.46218
4 1HPG BOC ALA ALA PRO GLU 0.002059 0.43801 8.02139
5 4YOI 4F4 0.002049 0.41862 8.49421
6 4SGA ACE PRO ALA PRO PHE 0.0008073 0.4326 8.83978
7 2Z48 NGA 0.008692 0.41447 8.88031
8 2Z48 A2G 0.02145 0.40097 8.88031
9 2OUA AES 0.00001147 0.56583 9.57447
10 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.0005808 0.4644 16.6667
11 4ZBY URA 0.02401 0.40245 16.6667
12 1UI0 URA 0.00867 0.42901 44.4444
13 1GJC 130 0.0000000008587 0.55991 45.0593
14 5A8Y VBM 0.000002354 0.54003 45.8716
15 1OSS BEN 0.0000000001889 0.80896 47.0852
16 1SQA UI1 0.000000002132 0.72685 47.3469
17 1RTF BEN 0.0000000000009055 0.67794 48.0159
18 3N7O N7O 0.0000002952 0.51239 48.6726
19 2AIQ BEN 0.00000001955 0.56433 48.9177
20 1FIW PBZ 0.00000000004648 0.68765 49.0347
21 1IAU ACE ILE GLU PRO ASJ 0.0000003266 0.59837 49.3392
22 1PQ7 ARG 0.000000003413 0.68665 49.5536
23 4NFE BEN 0.000000006676 0.56243 49.789
Pocket No.: 2; Query (leader) PDB : 1O0D; Ligand: 163; Similar sites found: 281
This union binding pocket(no: 2) in the query (biounit: 1o0d.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Y1A GSH 0.0009681 0.5045 None
2 1UO4 PIH 0.02431 0.41695 None
3 4F4S EFO 0.008395 0.40241 None
4 1Y9Q MED 0.0071 0.41628 1.04167
5 1G8S MET 0.0001616 0.4887 1.30435
6 3E6J DR2 0.03374 0.40598 1.31004
7 1ULE GLA GAL NAG 0.008764 0.42478 1.33333
8 2EB5 OXL 0.001618 0.44462 1.5444
9 5EQU AKG 0.01717 0.41079 1.5444
10 3KMT SAH 0.0018 0.4093 1.68067
11 3RF4 FUN 0.004445 0.41379 1.72414
12 1Y7P RIP 0.008284 0.42594 1.79372
13 2ZE3 AKG 0.0006916 0.45367 1.9305
14 2Q8H TF4 0.003795 0.45011 1.9305
15 1OMZ UD2 0.002423 0.42995 1.9305
16 2DVZ GLU 0.0009791 0.42915 1.9305
17 3R6K FUC GAL GLA 0.01899 0.40276 1.9305
18 1A59 CIT 0.01918 0.40256 1.9305
19 3PMD 11A 0.004027 0.40549 1.96078
20 1C3V PDC 0.006142 0.41332 2.04082
21 1PR9 NAP 0.004033 0.41068 2.04918
22 4AF5 CIT 0.0005479 0.46534 2.10526
23 3EW2 BTN 0.00447 0.40855 2.22222
24 4W6Z ETF 0.000237 0.50989 2.3166
25 4M5P MLA 0.001468 0.48046 2.3166
26 9LDT OXM 0.002208 0.47125 2.3166
27 3FW3 GLC 0.01448 0.46721 2.3166
28 9LDB OXM 0.004333 0.45604 2.3166
29 4NTD FAD 0.0005801 0.4484 2.3166
30 2JFV FLC 0.001613 0.44468 2.3166
31 1H2K OGA 0.002588 0.43563 2.3166
32 2BGM NAJ 0.003433 0.43418 2.3166
33 4B7E OGA 0.002074 0.4334 2.3166
34 2Y0I AKG 0.004469 0.4192 2.3166
35 4WX0 HXD 0.0008219 0.41684 2.3166
36 1ZFJ IMP 0.03001 0.41267 2.3166
37 1F74 NAY 0.0009924 0.40445 2.3166
38 1QDS PGA 0.001208 0.42564 2.39044
39 1YFZ IMP 0.006175 0.41322 2.43902
40 4DN8 BMA 0.003971 0.42743 2.5641
41 4B16 NAG 0.0003765 0.51113 2.7027
42 4KCT FDP 0.0009331 0.42464 2.7027
43 1I0Z OXM 0.01371 0.42233 2.7027
44 1V6A TRE 0.004858 0.41766 2.7027
45 1O68 KIV 0.004709 0.41275 2.7027
46 3RKR NAP 0.00227 0.41023 2.7027
47 4LO6 SIA GAL 0.02007 0.40452 2.7027
48 1R37 NAD 0.007202 0.40244 2.7027
49 1XX4 BAM 0.01023 0.40132 2.7027
50 1X8X TYR 0.005215 0.40116 2.7027
51 3CXO 1N5 0.006488 0.40053 2.7027
52 4EXO PYR 0.01414 0.41484 2.73973
53 2DTJ THR 0.0005948 0.43748 2.80899
54 4N7C AEF 0.02012 0.40161 2.84091
55 2WCV FUC 0.005348 0.40545 2.85714
56 1QB7 ADE 0.003811 0.40641 2.9661
57 2Y6P CTP 0.004313 0.40435 2.99145
58 3CBG 4FE 0.01647 0.42582 3.01724
59 3CBG FER 0.03594 0.40132 3.01724
60 4RJK PYR 0.003572 0.47059 3.0888
61 1F1V DHY 0.005018 0.40655 3.0888
62 2C31 ADP 0.02554 0.4062 3.0888
63 4JEJ 1GP 0.0004774 0.4355 3.27869
64 1NXJ GLV 0.003063 0.41508 3.27869
65 1Y13 BIO 0.0008296 0.43192 3.31492
66 2Q37 3AL 0.004147 0.42059 3.31492
67 4Q3F TLA 0.0163 0.4003 3.4188
68 1QH9 LAC 0.00533 0.42178 3.44828
69 2JC9 ADN 0.002145 0.4268 3.4749
70 1KYQ NAD 0.0002652 0.42157 3.4749
71 2VDJ HSE 0.01698 0.41103 3.4749
72 2HW1 FRU 0.008066 0.40827 3.4749
73 2DTX BMA 0.01144 0.40008 3.4749
74 1B74 DGN 0.01908 0.4086 3.54331
75 1L1Q 9DA 0.002015 0.4031 3.76344
76 3F81 STT 0.001305 0.47313 3.82514
77 3TKA CTN 0.000008064 0.62766 3.861
78 4LHM AZZ 0.007101 0.41063 3.861
79 4KOA NDP 0.0009556 0.41005 3.861
80 1RZM E4P 0.01635 0.40576 3.861
81 2J7T 274 0.005675 0.40006 3.861
82 1NF8 BOG 0.01388 0.40904 3.86473
83 2VQ5 LDP 0.01667 0.41808 3.9801
84 2VQ5 HBA 0.01907 0.40268 3.9801
85 3UIE ANP 0.002706 0.41215 4
86 1JN2 SFP 0.0001381 0.56186 4.21941
87 2NVK NAP 0.0005436 0.45129 4.2471
88 1UXG NAD 0.0008131 0.44282 4.2471
89 1UXG FUM 0.0008131 0.44282 4.2471
90 3B9Z CO2 0.00288 0.43358 4.2471
91 3FPZ AHZ 0.03408 0.40402 4.2471
92 1ZED PNP 0.01832 0.40349 4.2471
93 1YOA FMN 0.004876 0.46321 4.40252
94 4COQ SAN 0.007142 0.41617 4.45344
95 3IHB TRS 0.008965 0.46899 4.6332
96 1T3D CYS 0.005276 0.42833 4.6332
97 3IHB GLU 0.01115 0.41341 4.6332
98 2DKH 3HB 0.00526 0.41301 4.6332
99 1I9G SAM 0.01107 0.40607 4.6332
100 2CE7 ADP 0.002733 0.40273 4.6332
101 2HVW DDN 0.002155 0.40647 4.8913
102 3VPQ GSH 0.001677 0.43732 4.90196
103 1Y2W NAG 0.002682 0.43494 4.92958
104 2Z9V PXM 0.002431 0.42456 5.01931
105 2YVF NAD 0.02342 0.40314 5.01931
106 2YVF FAD 0.02261 0.40314 5.01931
107 1U7Z PMT 0.003296 0.41394 5.30973
108 1GU3 BGC BGC BGC BGC BGC 0.008551 0.40208 5.36913
109 1V7R CIT 0.005719 0.44977 5.37634
110 1RYD GLC 0.001843 0.44213 5.40541
111 2Q3M MLA 0.007578 0.43516 5.40541
112 3LM9 ADP 0.003057 0.4054 5.40541
113 4AMV F6R 0.001773 0.40509 5.40541
114 3UEC ALA ARG TPO LYS 0.0006755 0.4692 5.47945
115 2F01 BTQ 0.01329 0.41506 5.51181
116 2F01 BTN 0.01399 0.41415 5.51181
117 4NAO AKG 0.006855 0.42312 5.55556
118 4GYW UDP 0.002757 0.41557 5.55556
119 2OFD NGA 0.002381 0.43723 5.6338
120 2OFE NAG 0.00281 0.43405 5.6338
121 2ZSC BTN 0.002565 0.40372 5.67376
122 4M51 BEZ 0.005807 0.43331 5.79151
123 1Y42 TYR 0.00248 0.42421 5.79151
124 4USS GSH 0.002614 0.42327 5.79151
125 1NML CIT 0.00608 0.40818 5.79151
126 4A6F SEP 0.009472 0.43836 5.83333
127 1SS4 GSH 0.0005184 0.52499 5.88235
128 1SS4 CIT 0.02569 0.41699 5.88235
129 1XE7 GUN 0.009916 0.42934 5.91133
130 2O66 FLC 0.01132 0.40199 5.92593
131 3S9K CIT 0.002573 0.48249 5.9322
132 1JAC AMG 0.005213 0.45186 6.01504
133 1TUV VK3 0.0003145 0.50379 6.14035
134 1XHL NDP 0.0009938 0.432 6.17761
135 2QQF A1R 0.0009 0.42452 6.17761
136 1DSS NAD 0.0009908 0.42302 6.17761
137 4USQ FAD 0.004203 0.41121 6.17761
138 4O1M NAD 0.003791 0.40783 6.17761
139 3NNF AKG 0.01187 0.4064 6.17761
140 2IZ1 ATR 0.01257 0.4053 6.17761
141 3H86 AP5 0.004983 0.42504 6.25
142 3QDW NDG 0.0006864 0.46888 6.29371
143 3QDY CBS 0.001174 0.45822 6.29371
144 3QDW A2G 0.01344 0.42275 6.29371
145 1H8P PC 0.01531 0.41993 6.42202
146 2X2T GAL NGA 0.001912 0.46489 6.53595
147 2IMP NAI 0.03739 0.4023 6.56371
148 3WCS MAN NAG 0.0007464 0.44563 6.69291
149 3WCS MAN NAG GAL 0.001346 0.42383 6.69291
150 4LWM MHO 0.03208 0.40585 6.91244
151 1T26 GBD 0.0351 0.40888 6.94981
152 1T26 NAI 0.0351 0.40888 6.94981
153 4ME6 ADP 0.005998 0.41376 7.33591
154 1H8G CHT 0.004804 0.46357 7.36842
155 1WRA PC 0.007808 0.42052 7.72201
156 1QD0 RR6 0.003052 0.40543 7.8125
157 1WHT BZS 0.001156 0.45106 7.84314
158 1C1L GAL BGC 0.01035 0.41491 8.0292
159 2NCD ADP 0.003816 0.42213 8.10811
160 4B9E FAH 0.0001396 0.50051 8.33333
161 2XI7 XI7 0.002293 0.48109 8.33333
162 1O9U ADZ 0.001566 0.4692 8.33333
163 1Z44 NPO 0.02408 0.42521 8.33333
164 1RYI GOA 0.02589 0.42358 8.33333
165 1YBH P22 0.002271 0.41508 8.33333
166 1DXY COI 0.02443 0.40976 8.33333
167 2QLX RM4 0.01481 0.40774 8.33333
168 1WTC ACP 0.01651 0.40557 8.33333
169 1XOC VAL ASP SER LYS ASN THR SER SER TRP 0.008935 0.40517 8.33333
170 3ZPG 5GP 0.002267 0.46122 8.49421
171 2OWZ CIT 0.005838 0.42004 8.49421
172 3L6R MLI 0.01802 0.40382 8.49421
173 3GD8 BOG 0.02488 0.40305 8.52018
174 3SCH TB6 0.006246 0.41874 8.58586
175 1ZZ7 S0H 0.003995 0.41569 8.58586
176 4WBD ADP 0.0002313 0.49048 8.88031
177 4WBD CIT 0.004736 0.43753 8.88031
178 4F8L GAL 0.01363 0.4388 8.96552
179 4JCA CIT 0.02326 0.41796 8.98204
180 1KOL NAD 0.002021 0.42551 9.26641
181 1NU4 MLA 0.0001873 0.54037 9.27835
182 3R51 MMA 0.01161 0.42593 9.375
183 2BOI MFU 0.004605 0.41315 9.73451
184 1PTR PRB 0.001699 0.45087 10
185 3U4C NDP 0.004118 0.40515 10.0386
186 1SC3 MLI 0.0005416 0.48237 10.1124
187 1Y75 NAG 0.004673 0.40778 10.1695
188 3PNA CMP 0.003433 0.41311 10.3896
189 2BZ1 TAU 0.00261 0.47803 11.1111
190 3HZL 6PC 0.003456 0.45212 11.1111
191 3ZF8 GDP 0.0008756 0.43102 11.1111
192 4R33 TRP 0.001405 0.42774 11.1111
193 4R33 SAH 0.001405 0.42774 11.1111
194 2W8Q SIN 0.009844 0.4159 11.1111
195 2Y7P SAL 0.00492 0.41197 11.1111
196 4KCF AKM 0.002339 0.40632 11.1111
197 1C7S CBS 0.003271 0.4043 11.1111
198 1IYE PGU 0.0003156 0.44898 11.583
199 2BO4 FLC 0.02097 0.40077 11.583
200 2WCI GSH 0.004897 0.41751 12.5926
201 1JGS SAL 0.0139 0.43832 13.0435
202 1OGZ EQU 0.001645 0.41545 13.6
203 2V5E SCR 0.01131 0.43433 13.8614
204 1HFA PIO 0.0006664 0.51986 13.8889
205 1TDF NAP 0.0003172 0.48496 13.8889
206 1TDF FAD 0.0003231 0.46698 13.8889
207 3ZGE ASP 0.003275 0.44516 13.8889
208 2YD6 FLC 0.01745 0.43203 13.8889
209 1KC7 PPR 0.008865 0.41799 13.8889
210 3DG6 MUC 0.001214 0.4155 13.8889
211 4E28 9MZ 0.007643 0.41487 13.8889
212 2YLD CMO 0.009692 0.41031 13.8889
213 2NLI LAC 0.01634 0.4026 13.8889
214 2NLI FMN 0.01634 0.4026 13.8889
215 1ZJ6 G3D 0.004239 0.4001 13.8889
216 2VMD MBG 0.004214 0.44784 14.786
217 3BY8 MLT 0.002478 0.44337 14.7887
218 4LFL TG6 0.0006236 0.43669 14.8148
219 3T2W BTN 0.003876 0.40613 15.5738
220 2E1A MSE 0.002357 0.41961 16
221 3L24 GOA 0.0003907 0.49912 16.6667
222 1ZUW DGL 0.0001206 0.47091 16.6667
223 2ZWS PLM 0.003589 0.47047 16.6667
224 2AMV BIN 0.001032 0.45004 16.6667
225 3Q9T FAY 0.0007023 0.44525 16.6667
226 1H16 PYR 0.004101 0.44051 16.6667
227 3QV9 QV7 0.004131 0.42066 16.6667
228 4OYA 1VE 0.02437 0.41741 16.6667
229 1P9B HDA 0.005205 0.41638 16.6667
230 4CIB 7UZ 0.009469 0.4053 16.6667
231 4M7F BM3 0.00863 0.40192 16.6667
232 1PEA ACM 0.0008914 0.47207 18.9189
233 1DL7 NCH 0.02079 0.42872 19.4444
234 4IHQ ADP 0.001436 0.42817 19.4444
235 2DWU DGL 0.002027 0.42221 19.4444
236 4O8A 2OP 0.01485 0.4206 19.4444
237 1ECM TSA 0.002953 0.41572 19.4444
238 3TA2 AKG 0.002331 0.41419 19.4444
239 2OYS FMN 0.001142 0.41365 19.4444
240 1Q3Q ANP 0.01412 0.40947 19.4444
241 1PX8 XYP 0.008335 0.40767 19.4444
242 3LTW HLZ 0.001595 0.4449 22.2222
243 1GJW MAL 0.0006168 0.43687 22.2222
244 4G28 0W8 0.001708 0.42517 22.2222
245 2WQP WQP 0.001268 0.42079 22.2222
246 1GPJ CIT 0.00592 0.41977 22.2222
247 1UF5 CDT 0.001903 0.41803 22.2222
248 1GJW GLC 0.01093 0.41382 22.2222
249 3A1I UNU 0.003884 0.4061 22.2222
250 1I2B UPG 0.01736 0.40447 22.2222
251 1I2B NAD 0.01736 0.40447 22.2222
252 1I2B USQ 0.01736 0.40447 22.2222
253 4IVG ANP 0.002714 0.40403 22.2222
254 1T8U UAP SGN IDS SGN 0.01038 0.40071 22.2222
255 1BTN I3P 0.0166 0.43745 24.5283
256 4WVH ASP HIS ASP ALA HIS ALA 0.001054 0.43351 25
257 4P9Z NMI PTR 02K ASN NH2 0.003285 0.41919 25
258 2GWD GLU 0.003485 0.41285 25
259 1KYV RBF 0.0009958 0.40944 25
260 1T57 FMN 0.003149 0.40002 25
261 2XVE FAD 0.00337 0.4374 27.7778
262 1WDA BAG 0.002778 0.41677 27.7778
263 2XDQ MGX 0.02201 0.41203 27.7778
264 3JQ3 ADP 0.003365 0.4085 27.7778
265 2P69 PLP 0.008032 0.40835 27.7778
266 4TSK NDP 0.01685 0.40636 27.7778
267 1T10 F6P 0.0111 0.40235 27.7778
268 1BGQ RDC 0.004478 0.40098 27.7778
269 3BHO B4P 0.003991 0.45789 30.5556
270 2YIV YIV 0.00225 0.45293 30.5556
271 1R27 MGD 0.00343 0.41684 30.5556
272 1I1Q TRP 0.0008196 0.43785 33.3333
273 1FIQ MTE 0.001097 0.4276 33.3333
274 1FIQ SAL 0.002159 0.41951 33.3333
275 1U3I GSH 0.005155 0.41656 33.3333
276 1FIQ FAD 0.004232 0.41109 33.3333
277 3C1O NAP 0.003382 0.40228 33.3333
278 4DQ2 BTX 0.00496 0.4022 33.3333
279 4C2G ALA ALA ALA ALA 0.001121 0.43244 36.1111
280 3UDG TMP 0.002693 0.45751 38.8889
281 1EDO NAP 0.01009 0.42179 38.8889
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