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 15 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: 130
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP PHE GLU GLU ILE 1 1
2 ASP PHE SER ILE 0.746835 0.782609
3 ASP PHE GLU ASP TYR GLU PHE ASP 0.595745 0.744681
4 VAL ASN ASP ILE PHE GLU ALA ILE 0.590476 0.844444
5 THR ASN GLU PHE TYR PHE 0.582418 0.708333
6 THR ASN GLU PHE ALA PHE 0.582418 0.813953
7 ASP TRP GLU ILE VAL 0.558824 0.791667
8 GLU ILE ILE ASN PHE GLU LYS LEU 0.555556 0.829787
9 SER ILE ILE ASN PHE GLU LYS LEU 0.555556 0.764706
10 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.554545 0.8125
11 MET ASN GLU ASN ILE 0.554217 0.795455
12 GLY ALA PHE THR PHE ASN GLU ASP PHE 0.54902 0.714286
13 ASP PHE 0.546667 0.769231
14 THR ASN GLU TYR TYR VAL 0.543478 0.734694
15 GLU ASN GLN LYS GLU TYR PHE PHE 0.539216 0.673077
16 THR ASN GLU TYR LYS VAL 0.535354 0.74
17 ASP PHE M3L THR ASP 0.534653 0.655172
18 ACE 1PA GLU GLU ILE 0.533333 0.95
19 SER ILE ILE GLY PHE GLU LYS LEU 0.531532 0.795918
20 LEU GLU PHE GLN GLY 0.53125 0.822222
21 ALA GLU THR PHE 0.52809 0.837209
22 LEU ASP GLU GLU THR GLY GLU PHE LEU 0.522936 0.77551
23 ARG ABA GLN ILE PHE ALA ASN ILE 0.522523 0.866667
24 ACE VAL PHE PHE ALA GLU ASP NH2 0.520408 0.857143
25 PHE GLU ALA ASN GLY ASN LEU ILE 0.513274 0.77551
26 ALA LEU ASP LEU PHE 0.505882 0.875
27 ILE ASN PHE ASP PHE ASN THR ILE 0.504951 0.755102
28 THR ASN GLU PHE TYR ALA 0.504854 0.705882
29 SER GLU ILE GLU PHE ALA ARG LEU 0.504348 0.722222
30 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.503876 0.629032
31 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.5 0.729167
32 ASP ALA GLU PHE ARG HIS ASP SER 0.5 0.62069
33 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.5 0.619048
34 GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU 0.5 0.75
35 GLU THR LEU GLU ASP SER VAL PHE 0.5 0.723404
36 GLU GLN TYR LYS PHE TYR SER VAL 0.495413 0.660714
37 GLU THR LEU LEU ASP LEU ASP PHE LEU GLU 0.494845 0.857143
38 PHE LEU GLU LYS 0.494737 0.860465
39 PHE VAL PHE LEU GLU ILE NH2 0.485981 0.880952
40 GLU ASN PRO THR TYR LYS PHE PHE GLU GLN 0.485714 0.679245
41 THR TYR LYS PHE PHE GLU GLN 0.485714 0.679245
42 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.482143 0.791667
43 ALA GLU THR PHE TYR VAL ASP GLY 0.481481 0.72
44 ASP ALA ASP GLU TYR LEU 0.480392 0.804348
45 SER SER ILE GLU PHE ALA ARG LEU 0.478992 0.709091
46 ASP GLU LEU GLU ILE LYS ALA TYR 0.478261 0.795918
47 ASP ALA GLU PHE ARG HIS ASP 0.477477 0.62069
48 VAL GLN GLN GLU SER SER PHE VAL MET 0.477064 0.730769
49 SER ASP TYR GLN ARG LEU 0.47619 0.690909
50 ASP ALA ASP GLU FTY LEU NH2 0.475248 0.72549
51 MET ASN TYR ASP ILE 0.47191 0.818182
52 LYS GLN TRP ASP ASN TYR GLU PHE ILE TRP 0.469697 0.666667
53 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.466667 0.8125
54 LEU ASP GLU PTR VAL ALA THR ARG 0.465347 0.679245
55 LYS ALC LYS 0.465116 0.767442
56 GLY ALA GLU VAL PHE TYR VAL ASP GLY ALA 0.464912 0.692308
57 GLU ARG GLU SEP GLU PHE ASP ILE GLU ASP 0.464567 0.65
58 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.462185 0.76
59 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.461538 0.685185
60 ACE PTR GLU GLU ILE ACE 0.456311 0.716981
61 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.455285 0.672727
62 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.455285 0.633333
63 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.453846 0.622951
64 ALA ASN SER ARG VAL GLN ASP SER ILE ILE 0.453488 0.73913
65 ARG ABA VAL ILE PHE ALA ASN ILE 0.452991 0.75
66 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.452381 0.65
67 ARG ABA PHE ILE PHE ALA ASN ILE 0.452174 0.735849
68 TRP MET ASP PHE ASP ASP ASP ILE PRO PHE 0.451923 0.716981
69 TRP ASP ILE PRO PHE 0.451923 0.716981
70 TYR GLN PHE 0.451613 0.702128
71 SER HIS MET ALA GLU ILE 0.451327 0.655172
72 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.45082 0.685185
73 GLY ASP GLU VAL LYS VAL PHE ARG 0.449153 0.698113
74 ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.447368 0.703704
75 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.447154 0.716981
76 THR PHE LYS LYS THR ASN 0.446602 0.74
77 ACE MET GLU GLU VAL PHE 0.446602 0.804348
78 GLU ASN LEU TYR PHE GLN 0.444444 0.76
79 CYS THR PHE LYS THR LYS THR ASN 0.443396 0.711538
80 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA 0.441667 0.654545
81 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.441667 0.730769
82 ACE GLN PM3 GLU GLU ILE PRO 0.439655 0.612903
83 THR LYS ASN TYR LYS GLN PHE SER VAL 0.438596 0.649123
84 ILE ASP TRP PHE GLU GLY LYS GLU 0.4375 0.722222
85 MET ASN TRP ASN ILE 0.436893 0.72549
86 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.435484 0.678571
87 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.435484 0.684211
88 ASP GLU ASP LYS TRP ASP ASP PHE 0.432432 0.673077
89 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.431818 0.709091
90 LYS VAL ILE THR PHE ILE ASP LEU 0.431034 0.8125
91 TYR ASP GLN ILE LEU 0.429907 0.826087
92 GLU VAL ASN 1OL ALA GLU PHE 0.429752 0.826087
93 CYS VAL PHE MET 0.428571 0.723404
94 ILE ASP TRP PHE ASP GLY LYS GLU 0.426357 0.722222
95 ALA ILE PHE GLN SER SER MET THR LYS 0.42623 0.709091
96 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.42623 0.642857
97 SER GLN LEU LYS ASN ASN ALA LYS GLU ILE 0.424779 0.679245
98 GLY TYR GLN ASP TYR GLU PRO GLU ALA 0.422414 0.62069
99 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.421875 0.666667
100 ACE ASP ALA ASP GLU FTY LEU NH2 0.421053 0.711538
101 GLU THR VAL ARG PHE GLN SER ASP 0.420635 0.660714
102 ARG PRO GLY ASN PHE PHE GLN ASN ARG PRO 0.419048 0.666667
103 ACE PHE ASP GLU MET GLU GLU CYS 0.419048 0.808511
104 ASP GLU THR ASN LEU 0.418367 0.708333
105 ILE GLN GLN SER ILE GLU ARG ILE 0.418182 0.666667
106 GLU THR PHE TYR VAL ASP GLY 0.417391 0.666667
107 GLU LEU ASP 1OL VAL GLU PHE 0.416667 0.883721
108 GLY GLN VAL PRO PHE SER LYS GLU GLU CYS 0.415929 0.636364
109 ASP ASP TRP ASN TRP GLU VAL GLU ASP 0.415929 0.666667
110 GLU GLU GLN GLU GLU TYR 0.41573 0.772727
111 PRO GLU GLY ASP PM3 GLU GLU VAL LEU 0.415254 0.730769
112 ACE ILE TYR GLU SER LEU 0.415094 0.76
113 ACE ASN TRP GLU THR PHE 0.414634 0.642857
114 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.413793 0.730769
115 ALA TRP LEU PHE GLU ALA 0.413793 0.734694
116 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.412214 0.644068
117 GLU PHE SER PRO 0.411765 0.614035
118 GLY ALA GLN THR PHE TYR VAL ASP GLY ALA 0.411765 0.654545
119 LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE 0.410448 0.616667
120 ACE LEU PHE PHE GLK CF0 GLU 0.409524 0.782609
121 ARG ILE PHE SER 0.407407 0.692308
122 PRO GLU SEP LEU GLU SER CYS PHE 0.405172 0.660714
123 GLU VAL TYR GLU SER 0.403846 0.714286
124 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.403846 0.744681
125 PHE ARG TYR LEU GLY 0.403509 0.637931
126 HIS ILE PHE SER 0.401869 0.673469
127 ALA PHE 0.4 0.666667
128 ARG VAL LEU PHE GLU ALA MET 0.4 0.660714
129 MET PHE SER ILE ASP ASN ILE LEU ALA 0.4 0.703704
130 SER SER ARG LYS GLU TYR TYR ALA 0.4 0.62069
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: 26
This union binding pocket(no: 1) in the query (biounit: 1bhx.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UI0 URA 0.01222 0.41866 3.40136
2 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.0006862 0.4611 4.7619
3 4YOI 4F4 0.003131 0.41896 7.61905
4 4YLU R30 0.003917 0.41266 7.61905
5 2Z48 NGA 0.008531 0.41871 10.8844
6 2Z48 A2G 0.0217 0.40225 10.8844
7 1HPG BOC ALA ALA PRO GLU 0.002806 0.43172 14.2857
8 4SGA ACE PRO ALA PRO PHE 0.0008938 0.4301 15.2381
9 2OUA AES 0.00001285 0.57182 19.0476
10 5A8Y VBM 0.000003259 0.5498 39.4558
11 1RTF BEN 0.000000000003226 0.66413 44.2177
12 1IAU ACE ILE GLU PRO ASJ 0.0000003557 0.59671 44.2177
13 1OSS BEN 0.0000000001007 0.6341 44.7619
14 3N7O N7O 0.0000008259 0.49871 44.898
15 1PQ7 ARG 0.000000002343 0.66922 45.7143
16 2AIQ BEN 0.00000003724 0.55606 45.7143
17 5NB7 8NQ 0.0004866 0.46069 46.2585
18 1T32 OHH 0.0000002948 0.58134 46.9388
19 5FAH 5VT 0.00000004346 0.63529 47.619
20 1GJC 130 0.000000001536 0.55417 47.619
21 4NFE BEN 0.00000002592 0.5463 47.619
22 1ELE 0QN 0.00001899 0.46608 48.9796
23 1FIW PBZ 0.00000000007775 0.68049 49.5238
24 1SQA UI1 0.000000003632 0.71607 49.6599
25 4D8N 0HM 0.00000001509 0.65556 49.6599
26 1UTJ ABN 0.00000009392 0.62355 49.6599
Pocket No.: 2; Query (leader) PDB : 1BHX; Ligand: ASP PHE GLU GLU ILE; Similar sites found: 129
This union binding pocket(no: 2) in the query (biounit: 1bhx.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1O44 852 0.003427 0.45919 None
2 4R38 RBF 0.00458 0.43018 None
3 4EES FMN 0.007247 0.4205 None
4 5IXH OTP 0.01357 0.43209 1.36054
5 5DRB 5FJ 0.006788 0.44973 1.90476
6 5SVV FMN 0.01153 0.41069 3.80952
7 1SU2 ATP 0.0129 0.40464 3.80952
8 2Z6C FMN 0.008696 0.41481 3.87597
9 2HZQ STR 0.005114 0.42773 4.08163
10 5ML3 DL3 0.01701 0.42213 4.08163
11 2X4Z X4Z 0.0003475 0.5052 4.7619
12 5HCY 60D 0.003242 0.46464 4.7619
13 3WG3 A2G GAL NAG FUC 0.0008182 0.44488 4.7619
14 2NNQ T4B 0.03843 0.40463 4.7619
15 4XGX ADP 0.01411 0.40463 4.7619
16 2X2M X2M 0.01854 0.40229 4.7619
17 2YNE NHW 0.002416 0.49064 5.44218
18 2YNE YNE 0.002416 0.49064 5.44218
19 4MNS 2AX 0.04342 0.40938 5.44218
20 4NS0 PIO 0.0006519 0.47347 5.71429
21 1ULE GLA GAL NAG 0.003894 0.43041 5.71429
22 5IXG OTP 0.0431 0.40801 5.71429
23 3MTX PGT 0.0309 0.40764 6.12245
24 5HA0 LTD 0.005478 0.43474 6.66667
25 4GCZ FMN 0.00581 0.42328 6.66667
26 3TAY MN0 0.008777 0.42305 6.66667
27 2E27 AB0 0.00265 0.42004 6.66667
28 1Z06 GNP 0.02111 0.40262 6.66667
29 5TFZ 7BC 0.007354 0.40226 6.66667
30 2JEN GLC GLC BGC XYS BGC XYS 0.001339 0.45805 6.80272
31 3SAO NKN 0.002582 0.43371 6.80272
32 2I6A 5I5 0.01534 0.40633 6.80272
33 4XIZ LPP 0.0006634 0.48952 7.48299
34 5BYZ 4WE 0.0002857 0.50509 7.61905
35 4I4S LAT 0.006442 0.42475 7.61905
36 5I0U DCY 0.005629 0.41289 7.61905
37 1GT4 UNA 0.01104 0.40588 7.61905
38 2PYW ADP 0.01527 0.40473 7.61905
39 4Q0L V14 0.02508 0.40174 7.61905
40 1ZHX HC3 0.006465 0.43116 8.16327
41 1ECC PCP 0.02999 0.42028 8.16327
42 4M26 SIN 0.01844 0.40845 8.16327
43 3RI1 3RH 0.01899 0.4078 8.16327
44 2WEI VGG 0.01252 0.40119 8.16327
45 4Y24 TD2 0.004789 0.41617 8.44156
46 3E7O 35F 0.008166 0.4316 8.57143
47 4CSV STI 0.005725 0.429 8.57143
48 2XMY CDK 0.000813 0.51222 8.84354
49 2YAK OSV 0.0004906 0.49172 8.84354
50 4HIA FMN 0.005939 0.44351 9.52381
51 4IPH 1FJ 0.004509 0.43739 9.52381
52 2HGS ADP 0.01617 0.40683 9.52381
53 2WSA MYA 0.006717 0.47194 10
54 2WSA 646 0.006717 0.47194 10
55 2EQA AMP 0.0238 0.40149 10
56 5EW9 5VC 0.03714 0.43635 10.2041
57 4M1U A2G MBG 0.0002122 0.41266 10.2041
58 5JFS 6K0 0.006869 0.44461 10.4762
59 3G5N PB2 0.02065 0.43823 10.4762
60 3S7O LBV 0.02326 0.40968 10.4762
61 1T27 PCW 0.0373 0.40891 10.4762
62 1C1L GAL BGC 0.01382 0.40371 10.4762
63 5DKK FMN 0.01705 0.40063 10.4762
64 5IH9 6BF 0.000271 0.5121 11.4286
65 4OTH DRN 0.008688 0.41843 11.4286
66 5UR1 YY9 0.02879 0.40378 11.4286
67 5FBN 5WF 0.006393 0.4407 12.2449
68 3GNE FLC 0.008255 0.41951 12.2449
69 5JGA 6KC 0.0158 0.41827 12.2449
70 5EOB 5QQ 0.002673 0.47727 12.381
71 1GQG DCD 0.002298 0.44845 12.381
72 4CQE CQE 0.006485 0.44379 12.381
73 4XUC SAM 0.0351 0.40373 12.381
74 4XUC 43G 0.0351 0.40373 12.381
75 3F9W SAH 0.01788 0.40621 13.3333
76 5AIG VPR 0.01089 0.4038 13.6
77 4ITH RCM 0.0006642 0.47289 13.6054
78 5ISY NAD 0.001686 0.43997 13.6054
79 4WW7 AMP 0.007616 0.42122 14.2857
80 1J3R 6PG 0.003497 0.42255 15.2381
81 2PTZ PAH 0.0336 0.40769 15.2381
82 3PUR 2HG 0.01347 0.40706 15.6463
83 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 0.00001826 0.41312 15.7895
84 5A5W GUO 0.004417 0.45561 16.1905
85 4YLL 4E3 0.01686 0.40593 16.1905
86 4QJP V1F 0.02089 0.40432 16.1905
87 3EPO MP5 0.005941 0.42281 16.3265
88 3SXF BK5 0.0009494 0.48296 16.6667
89 4UWJ MYA 0.003092 0.48144 16.6667
90 4UWJ 7L5 0.003092 0.48144 16.6667
91 5F3I 5UJ 0.03796 0.41615 16.6667
92 3QCQ 3Q0 0.00021 0.5563 17.0068
93 1OI6 TMP 0.00756 0.42053 17.0068
94 1CM8 ANP 0.01437 0.40041 17.0068
95 2TPS TPS 0.01423 0.41407 17.1429
96 4LIT AKG 0.004184 0.40013 17.6871
97 5DJT FMN 0.008734 0.41472 18.0328
98 4CLI 5P8 0.007142 0.4467 18.0952
99 1MH5 HAL 0.006271 0.43029 18.0952
100 4FFG LBS 0.001828 0.41354 18.3673
101 4OMJ 2TX 0.03508 0.40163 18.3673
102 1I82 BGC BGC 0.001235 0.41791 19.0476
103 4BVA T3 0.01918 0.4214 19.7279
104 4FG8 ATP 0.01534 0.40464 19.7279
105 2JDR L20 0.00516 0.46359 20
106 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.00516 0.46359 20
107 4GJ3 0XP 0.008984 0.42949 20
108 5U98 1KX 0.02396 0.41729 20
109 1ND2 MYR 0.006314 0.41531 20
110 2CM4 RCL 0.0005693 0.4001 20
111 1KHZ ADV 0.02203 0.40317 22.449
112 4CJN QNZ 0.008051 0.41939 23.3333
113 2HK5 1BM 0.0189 0.40021 23.8095
114 2XN5 FUN 0.006984 0.40851 25.7143
115 2GJ5 VD3 0.006144 0.445 26.6667
116 5HES 032 0.004701 0.43145 26.6667
117 2FB3 GTP 0.01027 0.42527 26.6667
118 2XG5 EC2 0.005508 0.43458 29.5238
119 2XG5 EC5 0.005508 0.43458 29.5238
120 4UAL 3FV 0.01443 0.40228 29.932
121 4C2V YJA 0.001534 0.46683 30
122 5EYK 5U5 0.002005 0.45801 30
123 5C03 AGS 0.009009 0.41214 30
124 4ZSI GLP 0.0107 0.40655 30
125 2YAB AMP 0.01068 0.41049 33.3333
126 5N87 N66 0.002714 0.46092 36.6667
127 5I8T LAC 0.003949 0.4106 36.6667
128 1OLM VTQ 0.009515 0.42423 40
129 1OBD ATP 0.007932 0.40833 43.3333
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