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Receptor
PDB id Resolution Class Description Source Keywords
1BHX 2.3 Å EC: 3.4.21.5 X-RAY STRUCTURE OF THE COMPLEX OF HUMAN ALPHA THROMBIN WITH INHIBITOR SDZ 229-357 HOMO SAPIENS SERINE PROTEASE
Ref.: RATIONAL DESIGN, SYNTHESIS, AND X-RAY STRUCTURE OF NONCOVALENT THROMBIN INHIBITORS. J.MED.CHEM. V. 41 3664 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ASP PHE GLU GLU ILE E:55;
Valid;
none;
submit data
648.646 n/a O=C([...
R56 F:1;
Valid;
none;
Ki = 0.145 uM
468.593 C19 H28 N6 O4 S2 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1BHX 2.3 Å EC: 3.4.21.5 X-RAY STRUCTURE OF THE COMPLEX OF HUMAN ALPHA THROMBIN WITH INHIBITOR SDZ 229-357 HOMO SAPIENS SERINE PROTEASE
Ref.: RATIONAL DESIGN, SYNTHESIS, AND X-RAY STRUCTURE OF NONCOVALENT THROMBIN INHIBITORS. J.MED.CHEM. V. 41 3664 1998
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 1BHX Ki = 0.145 uM R56 C19 H28 N6 O4 S2 c1ccc(cc1)....
2 3PO1 Kd = 95 uM MKY C12 H14 N4 O3 S [H]/N=C(N)....
3 2PKS ic50 = 11 uM G44 C21 H20 N4 O [H]/N=C(c1....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 1BHX Ki = 0.145 uM R56 C19 H28 N6 O4 S2 c1ccc(cc1)....
2 3PO1 Kd = 95 uM MKY C12 H14 N4 O3 S [H]/N=C(N)....
3 2PKS ic50 = 11 uM G44 C21 H20 N4 O [H]/N=C(c1....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1BHX Ki = 0.145 uM R56 C19 H28 N6 O4 S2 c1ccc(cc1)....
2 3PO1 Kd = 95 uM MKY C12 H14 N4 O3 S [H]/N=C(N)....
3 2PKS ic50 = 11 uM G44 C21 H20 N4 O [H]/N=C(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ASP PHE GLU GLU ILE; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP PHE GLU GLU ILE 1 1
2 ASP PHE GLU ASP TYR GLU PHE ASP 0.619565 0.74
3 ACE 1PA GLU GLU ILE 0.607143 0.926829
4 THR ASN GLU PHE ALA PHE 0.588889 0.818182
5 VAL ASN ASP ILE PHE GLU ALA ILE 0.580952 0.866667
6 THR ASN GLU PHE TYR PHE 0.571429 0.714286
7 ASP ALA GLU PHE ARG HIS ASP 0.568627 0.77551
8 ASP PHE 0.554054 0.825
9 MET ASN GLU ASN ILE 0.548781 0.818182
10 ASP TRP GLU ILE VAL 0.543689 0.795918
11 ASP PHE M3L THR ASP 0.54 0.661017
12 LEU GLU PHE GLN GLY 0.536842 0.844444
13 THR ASN GLU TYR TYR VAL 0.532609 0.74
14 ALA GLU THR PHE 0.522727 0.840909
15 GLU ILE ILE ASN PHE GLU LYS LEU 0.522523 0.833333
16 ILE ASN PHE ASP PHE ASN THR ILE 0.520408 0.77551
17 SER ILE ILE ASN PHE GLU LYS LEU 0.517857 0.784314
18 ACE VAL PHE PHE ALA GLU ASP NH2 0.515464 0.860465
19 THR ASN GLU TYR LYS VAL 0.514852 0.730769
20 LEU ASP GLU GLU THR GLY GLU PHE LEU 0.513761 0.78
21 ARG ABA GLN ILE PHE ALA ASN ILE 0.513514 0.888889
22 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.513043 0.816327
23 ALA LEU ASP LEU PHE 0.511905 0.878049
24 GLU ASN GLN LYS GLU TYR PHE PHE 0.509615 0.666667
25 GLU THR LEU GLU ASP SER VAL PHE 0.505618 0.729167
26 ACE PHE ASP GLU MET GLU GLU CYS 0.505155 0.791667
27 THR ASN GLU PHE TYR ALA 0.5 0.72549
28 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.496124 0.634921
29 GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU 0.495935 0.754717
30 ASP ALA GLU PHE ARG HIS ASP SER 0.495726 0.637931
31 PHE GLU ALA ASN GLY ASN LEU ILE 0.495575 0.795918
32 ACE MET GLU GLU VAL PHE 0.489583 0.787234
33 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.488722 0.625
34 SER GLU ILE GLU PHE ALA ARG LEU 0.487179 0.740741
35 SER ILE ILE GLY PHE GLU LYS LEU 0.486957 0.8
36 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.486486 0.78
37 VAL GLN GLN GLU SER SER PHE VAL MET 0.481481 0.75
38 ASP ALA ASP GLU TYR LEU 0.480392 0.808511
39 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.475728 0.770833
40 PHE VAL PHE LEU GLU ILE NH2 0.472222 0.883721
41 GLU ASN PRO THR TYR LYS PHE PHE GLU GLN 0.471698 0.685185
42 THR TYR LYS PHE PHE GLU GLN 0.471698 0.685185
43 LEU ASP GLU PTR VAL ALA THR ARG 0.47 0.685185
44 GLU GLN TYR LYS PHE TYR SER VAL 0.469027 0.678571
45 SER ASP TYR GLN ARG LEU 0.46729 0.709091
46 GLY ALA GLU VAL PHE TYR VAL ASP GLY ALA 0.464912 0.698113
47 SER SER ILE GLU PHE ALA ARG LEU 0.46281 0.727273
48 ASP GLU LEU GLU ILE LYS ALA TYR 0.461538 0.784314
49 ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.460177 0.722222
50 GLU ARG GLU SEP GLU PHE ASP ILE GLU ASP 0.449612 0.666667
51 MET ASN TYR ASP ILE 0.449438 0.822222
52 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.447154 0.690909
53 THR PHE LYS LYS THR ASN 0.446602 0.745098
54 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.446281 0.78
55 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA 0.445378 0.660714
56 CYS VAL PHE MET 0.443299 0.729167
57 TRP ASP ILE PRO PHE 0.442308 0.740741
58 TRP MET ASP PHE ASP ASP ASP ILE PRO PHE 0.442308 0.740741
59 CYS THR PHE LYS THR LYS THR ASN 0.439252 0.730769
60 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.439024 0.709091
61 ALA ILE PHE GLN SER SER MET THR LYS 0.438017 0.727273
62 ARG ABA PHE ILE PHE ALA ASN ILE 0.435897 0.754717
63 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.435484 0.816327
64 LYS GLN TRP ASP ASN TYR GLU PHE ILE TRP 0.432836 0.684211
65 ACE ASP ALA ASP GLU FTY LEU NH2 0.432432 0.716981
66 ASP ALA ASP GLU FTY LEU NH2 0.432432 0.716981
67 TYR GLN PHE 0.430108 0.723404
68 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.429752 0.735849
69 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.428571 0.65
70 ACE ILE TYR GLU SER LEU 0.428571 0.745098
71 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.428571 0.684211
72 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.428571 0.703704
73 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.428571 0.696429
74 ACE GLN PM3 GLU GLU ILE PRO 0.42735 0.629032
75 GLU ASN LEU TYR PHE GLN 0.427273 0.78
76 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.426357 0.666667
77 ARG ABA VAL ILE PHE ALA ASN ILE 0.425 0.769231
78 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.424242 0.629032
79 MET ASN TRP ASN ILE 0.423077 0.745098
80 ASP ARG VAL TYR 0.42268 0.847826
81 GLY TYR GLN ASP TYR GLU PRO GLU ALA 0.422414 0.627119
82 ARG PRO GLY ASN PHE PHE GLN ASN ARG PRO 0.419048 0.686275
83 THR LYS ASN TYR LYS GLN PHE SER VAL 0.418803 0.666667
84 GLU VAL ASN 1OL ALA GLU PHE 0.418033 0.847826
85 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.418033 0.703704
86 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.41791 0.714286
87 ILE ASP TRP PHE GLU GLY LYS GLU 0.416667 0.727273
88 GLU LEU ASP 1OL VAL GLU PHE 0.416667 0.886364
89 ACE ILE GLU SER THR GLU ILE 0.416667 0.75
90 SER TRP PHE GLN THR ASP LEU 0.414062 0.655172
91 ASP GLU 0.413333 0.775
92 ACE PTR GLU DIP 0.412371 0.745098
93 GLU THR PHE TYR VAL ASP GLY 0.412281 0.672727
94 SER GLN LEU LYS ASN ASN ALA LYS GLU ILE 0.412281 0.698113
95 ASP ASP TRP ASN TRP GLU VAL GLU ASP 0.412281 0.685185
96 ACE ASN TRP GLU THR PHE 0.411765 0.660714
97 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.411765 0.75
98 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.41129 0.660714
99 GLY ASP GLU VAL LYS VAL PHE ARG 0.41129 0.716981
100 SER LEU ARG PHE LEU TYR GLU GLY 0.409836 0.639344
101 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.409449 0.701754
102 ILE GLN GLN SER ILE GLU ARG ILE 0.409091 0.685185
103 PRO GLU SEP LEU GLU SER CYS PHE 0.408696 0.666667
104 GLU THR VAL ARG PHE GLN SER ASP 0.408 0.690909
105 GLU PHE SER PRO 0.407767 0.62069
106 ACE PTR GLU GLU ILE GLU 0.407767 0.703704
107 LEU PRO SER PHE GLU THR ALA LEU 0.40625 0.629032
108 ILE ASP TRP PHE ASP GLY LYS GLU 0.406015 0.727273
109 TYR ASP GLN ILE LEU 0.40566 0.847826
110 ASP GLU ASP LYS TRP ASP ASP PHE 0.405172 0.666667
111 ALA PHE 0.405063 0.725
112 GLY ALA GLN THR PHE TYR VAL ASP GLY ALA 0.403361 0.672727
113 LYS VAL ILE THR PHE ILE ASP LEU 0.403361 0.8
114 MET PHE SER ILE ASP ASN ILE LEU ALA 0.4 0.722222
115 PRO GLU GLY ASP PM3 GLU GLU VAL LEU 0.4 0.735849
116 PHE ALA GLN 0.4 0.85
Ligand no: 2; Ligand: R56; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 R56 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1BHX; Ligand: R56; Similar sites found with APoc: 35
This union binding pocket(no: 1) in the query (biounit: 1bhx.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 1UI0 URA 3.40136
2 3MMG GLU THR VAL ARG PHE GLN SER ASP 4.7619
3 1SZ2 BGC 4.7619
4 3NOJ PYR 5.71429
5 1RDL MMA 6.66667
6 6DEF GCP 6.66667
7 2UXR ICT 7.48299
8 4YOI 4F4 7.61905
9 6FFK D7Z 7.61905
10 4YLU R30 7.61905
11 2XYA 7L4 9.52381
12 2Z48 NGA 10.8844
13 2Z48 A2G 10.8844
14 1HPG BOC ALA ALA PRO GLU 14.2857
15 4SGA ACE PRO ALA PRO PHE 15.2381
16 2OUA AES 19.0476
17 4X7R NTO 26.6667
18 5A8Y VBM 39.4558
19 1RTF BEN 44.2177
20 1IAU ACE ILE GLU PRO ASJ 44.2177
21 1OSS BEN 44.7619
22 3N7O N7O 44.898
23 1PQ7 ARG 45.7143
24 2AIQ BEN 45.7143
25 6B74 BEN 46.2585
26 5NB7 8NQ 46.2585
27 1T32 OHH 46.9388
28 5ZFI 9C9 47.619
29 5FAH 5VT 47.619
30 1GJC 130 47.619
31 4NFE BEN 47.619
32 1FIW PBZ 49.5238
33 1UTJ ABN 49.6599
34 1SQA UI1 49.6599
35 4D8N 0HM 49.6599
Pocket No.: 2; Query (leader) PDB : 1BHX; Ligand: ASP PHE GLU GLU ILE; Similar sites found with APoc: 242
This union binding pocket(no: 2) in the query (biounit: 1bhx.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4R38 RBF None
2 4EES FMN None
3 5IXH OTP 1.36054
4 5DRB 5FJ 1.90476
5 2QX0 PH2 2.04082
6 1Y7P RIP 2.72109
7 5T7I LAT NAG GAL 2.72109
8 3P7N FMN 2.85714
9 4O9S 2RY 3.25581
10 2AG4 LP3 3.80952
11 2AG4 OLA 3.80952
12 5SVV FMN 3.80952
13 5GP0 GPP 3.80952
14 1SU2 ATP 3.80952
15 2Z6C FMN 3.87597
16 3E8N ATP 4.08163
17 3E8N VRA 4.08163
18 2HZQ STR 4.08163
19 5ML3 DL3 4.08163
20 6CAY ERG 4.08163
21 4WVW SLT 4.16667
22 5HCY 60D 4.7619
23 3WG3 A2G GAL NAG FUC 4.7619
24 4P8K 38C 4.7619
25 6C0T EE4 4.7619
26 5FYR INS 4.7619
27 1SDW IYT 4.7619
28 5D48 L96 4.7619
29 5XVG 8FX 4.7619
30 2NNQ T4B 4.7619
31 4XGX ADP 4.7619
32 2X2M X2M 4.7619
33 3NV3 GAL NAG MAN 5.07246
34 2YNE NHW 5.44218
35 2YNE YNE 5.44218
36 4RYV ZEA 5.44218
37 4MNS 2AX 5.44218
38 4NS0 PIO 5.71429
39 1ULE GLA GAL NAG 5.71429
40 4WUJ FMN 5.71429
41 5IXG OTP 5.71429
42 1IS3 LAT 5.71429
43 3WUC GLC GAL 5.71429
44 3MTX PGT 6.12245
45 3E2M E2M 6.12245
46 6GG9 FMN 6.17284
47 5HA0 LTD 6.66667
48 5MU6 KFK 6.66667
49 5MU6 MYA 6.66667
50 4U03 GTP 6.66667
51 4U03 TLL 6.66667
52 4GCZ FMN 6.66667
53 2GC0 PAN 6.66667
54 2E27 AB0 6.66667
55 5TFZ 7BC 6.66667
56 3LF0 ATP 6.66667
57 1Z06 GNP 6.66667
58 2OG7 SIN 6.66667
59 5HCF BGC 6.66667
60 3BJE URA 6.66667
61 3ETG NDP 6.66667
62 3ETG GLU 6.66667
63 1OFZ FUC 6.66667
64 2JLD AG1 6.80272
65 5M90 JIF 6.80272
66 3SAO NKN 6.80272
67 2JEN GLC GLC BGC XYS BGC XYS 6.80272
68 3FHR P4O 6.80272
69 2I6A 5I5 6.80272
70 2PR5 FMN 6.81818
71 4XIZ LPP 7.48299
72 4WVO 3UZ 7.48299
73 5JSP DQY 7.48299
74 2ABS ACP 7.48299
75 6C1S EFV 7.61905
76 5I0U DCY 7.61905
77 5XWC 8GL 7.61905
78 5XWC NAP 7.61905
79 5XWC 2IT 7.61905
80 3ORK AGS 7.61905
81 1GT4 UNA 7.61905
82 2PYW ADP 7.61905
83 5IDB BMA 7.61905
84 1ZHX HC3 8.16327
85 2YG3 FAD 8.16327
86 4M26 ZZU 8.16327
87 4M26 SIN 8.16327
88 3RI1 3RH 8.16327
89 2WEI VGG 8.16327
90 4Y24 TD2 8.44156
91 3E7O 35F 8.57143
92 4CSV STI 8.57143
93 6GNO XDI 8.57143
94 5TBM 79A 8.57143
95 1I7E IBS 8.57143
96 2R5T ANP 8.57143
97 2HRL SIA GAL SIA BGC NGA CEQ 8.57143
98 2XMY CDK 8.84354
99 2YAK OSV 8.84354
100 4G0P U5P 8.84354
101 1LLU NAD 8.84354
102 5FPX GLY SER SER HIS HIS HIS HIS HIS 8.84956
103 4IPH 1FJ 9.52381
104 4HIA FMN 9.52381
105 5FU3 BGC BGC BGC 9.52381
106 5ZFJ 9BF 9.52381
107 2PVN P63 9.52381
108 5GUD 2IT 9.52381
109 5GUD NDP 9.52381
110 4KS7 X4Z 9.52381
111 4YVN EBS 9.52381
112 2HGS ADP 9.52381
113 6EXF LYS 9.52381
114 2WSA 646 10
115 2WSA MYA 10
116 2EQA AMP 10
117 4M1U A2G MBG 10.2041
118 5H9P TD2 10.2041
119 5JFS 6K0 10.4762
120 3G5N PB2 10.4762
121 5GLT BGC GAL NAG GAL 10.4762
122 6BU0 IHP 10.4762
123 1T27 PCW 10.4762
124 1C1L GAL BGC 10.4762
125 1G8K MGD 10.4762
126 5DKK FMN 10.4762
127 5ODY 9SK 10.8696
128 4KBA 1QM 10.8844
129 5OKT 9XK 10.8844
130 2WKQ FMN 10.8844
131 5IH9 6BF 11.4286
132 5UR1 YY9 11.4286
133 3PP0 03Q 11.4286
134 4OTH DRN 11.4286
135 4OJ8 AKG 11.4286
136 1H2B NAJ 11.5646
137 5FBN 5WF 12.2449
138 3GNE FLC 12.2449
139 1DZK PRZ 12.2449
140 5JGA 6KC 12.2449
141 2A92 NAI 12.2449
142 2QL9 CIT 12.3711
143 5EOB 5QQ 12.381
144 1GQG DCD 12.381
145 4CQE CQE 12.381
146 4XUC 43G 12.381
147 4XUC SAM 12.381
148 1TT8 PHB 12.9252
149 6GBV FMN 13.0137
150 5OCG 9R5 13.3333
151 5U55 S0H 13.3333
152 5OES ADP 13.3333
153 6FA4 D1W 13.3333
154 5AIG VPR 13.6
155 5ISY NAD 13.6054
156 1IR3 ANP 13.6054
157 4ITH RCM 13.6054
158 4WW7 AMP 14.2857
159 5NLD LBT 14.2857
160 3VV1 GAL FUC 14.2857
161 1Y0G 8PP 14.966
162 1J3R 6PG 15.2381
163 4D52 GXL 15.6463
164 4D52 GIV 15.6463
165 3PUR 2HG 15.6463
166 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 15.7895
167 5A5W GUO 16.1905
168 3SCH TB6 16.1905
169 1ZZ7 S0H 16.1905
170 6A1G 9OL 16.1905
171 5E2N V14 16.1905
172 3EPO MP5 16.3265
173 4UWJ 7L5 16.6667
174 4UWJ MYA 16.6667
175 5F3I 5UJ 16.6667
176 4UXL 5P8 17.0068
177 1OI6 TMP 17.0068
178 1CM8 ANP 17.0068
179 5DEY 59T 17.1429
180 2TPS TPS 17.1429
181 2GOO NDG 17.5573
182 4LIT AKG 17.6871
183 1XE7 GUN 17.6871
184 5DJT FMN 18.0328
185 5DJU FMN 18.0328
186 4CLI 5P8 18.0952
187 1MH5 HAL 18.0952
188 1IA9 ANP 18.0952
189 5H9Q TD2 18.0952
190 4FFG LBS 18.3673
191 5Y6Q MCN 18.3673
192 4OMJ 2TX 18.3673
193 1I82 BGC BGC 19.0476
194 4BVA T3 19.7279
195 4FG8 ATP 19.7279
196 4Q5H ANP 19.7368
197 2CM4 RCL 20
198 2JDR L20 20
199 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 20
200 3C0G 3AM 20
201 5U98 1KX 20
202 5DQ8 FLF 20
203 4GJ3 0XP 20
204 1KHZ ADV 22.449
205 2ET1 GLV 23.3333
206 5LGD PLM 23.3333
207 4CJN QNZ 23.3333
208 6EZ6 C5Z 23.3333
209 6GWR FEW 23.8095
210 2HKA C3S 23.8095
211 2HK5 1BM 23.8095
212 2XN3 ID8 25
213 2XN5 FUN 25.7143
214 2BOS GLA GAL 26.6667
215 2BOS GLA GAL GLC 26.6667
216 5HES 032 26.6667
217 2FB3 GTP 26.6667
218 2GJ5 VD3 26.6667
219 4DC2 ADE 27.619
220 5XQW 8EU 27.8912
221 2XG5 EC5 29.5238
222 2XG5 EC2 29.5238
223 4C2V YJA 30
224 5EYK 5U5 30
225 4S28 SAH 30
226 4S28 AIR 30
227 5C03 AGS 30
228 5T8O 76Z 30
229 4ZSI GLP 30
230 5W0N UPU 30
231 5YZC NAG 30
232 3QRC SCR 30.4762
233 3BGD PM6 33.3333
234 3IGO ANP 33.3333
235 2YAB AMP 33.3333
236 5N87 N66 36.6667
237 5I8T LAC 36.6667
238 1OLM VTQ 40
239 6ES0 BW8 40
240 6EQS BV8 40
241 1OBD ATP 43.3333
242 6GQM F8H 46.6667
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