Receptor
PDB id Resolution Class Description Source Keywords
1D9I 2.3 Å EC: 3.4.21.5 STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTOPHI INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1 HOMO SAPIENS GLOBULAR HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTROPHILIC INHIBITORS HAVING CYCLOHEXYL MOIE P1. ACTA CRYSTALLOGR.,SECT.D V. 56 294 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
00P A:380;
Valid;
none;
Ki = 0.78 nM
475.561 C22 H29 N5 O5 S c1ccc...
ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU I:355;
Valid;
none;
submit data
1271.32 n/a [S+2]...
NA A:950;
A:951;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1D9I 2.3 Å EC: 3.4.21.5 STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTOPHI INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1 HOMO SAPIENS GLOBULAR HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTROPHILIC INHIBITORS HAVING CYCLOHEXYL MOIE P1. ACTA CRYSTALLOGR.,SECT.D V. 56 294 2000
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 1D9I Ki = 0.78 nM 00P C22 H29 N5 O5 S c1ccc(cc1)....
2 1JWT Ki = 14 nM BLI C22 H32 N6 O5 S c1ccc(cc1)....
3 1XM1 - GAH C38 H61 N11 O6 [H]/N=C(N)....
4 1HAG - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
5 1ZGV ic50 ~ 1 uM 501 C17 H21 Cl N6 CCCCNc1cc(....
6 2BDY ic50 = 0.017 uM UNB C27 H26 N4 O4 S [H]/N=C(c1....
7 1G37 - PHE GLU ALA ILE PRO ALA GLU TYR LEU n/a n/a
8 1ZGI Ki = 4.6 uM 382 C22 H23 F2 N7 O c1ccc(c(c1....
9 1D6W Ki = 1100 nM 00R C24 H29 N7 O5 S c1ccc(cc1)....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 1D9I Ki = 0.78 nM 00P C22 H29 N5 O5 S c1ccc(cc1)....
2 1JWT Ki = 14 nM BLI C22 H32 N6 O5 S c1ccc(cc1)....
3 1XM1 - GAH C38 H61 N11 O6 [H]/N=C(N)....
4 1HAG - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
5 1ZGV ic50 ~ 1 uM 501 C17 H21 Cl N6 CCCCNc1cc(....
6 2BDY ic50 = 0.017 uM UNB C27 H26 N4 O4 S [H]/N=C(c1....
7 1G37 - PHE GLU ALA ILE PRO ALA GLU TYR LEU n/a n/a
8 1ZGI Ki = 4.6 uM 382 C22 H23 F2 N7 O c1ccc(c(c1....
9 1D6W Ki = 1100 nM 00R C24 H29 N7 O5 S c1ccc(cc1)....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 1D9I Ki = 0.78 nM 00P C22 H29 N5 O5 S c1ccc(cc1)....
2 1JWT Ki = 14 nM BLI C22 H32 N6 O5 S c1ccc(cc1)....
3 1XM1 - GAH C38 H61 N11 O6 [H]/N=C(N)....
4 1HAG - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
5 1ZGV ic50 ~ 1 uM 501 C17 H21 Cl N6 CCCCNc1cc(....
6 2BDY ic50 = 0.017 uM UNB C27 H26 N4 O4 S [H]/N=C(c1....
7 1G37 - PHE GLU ALA ILE PRO ALA GLU TYR LEU n/a n/a
8 1ZGI Ki = 4.6 uM 382 C22 H23 F2 N7 O c1ccc(c(c1....
9 1D6W Ki = 1100 nM 00R C24 H29 N7 O5 S c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 00P; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 00P 1 1
2 IH1 0.652632 0.882353
3 00R 0.542857 0.915663
Ligand no: 2; Ligand: ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU; Similar ligands found: 85
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU 1 1
2 ASP PHE GLU GLU ILE PRO GLU GLU TYS 0.785714 0.973684
3 ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU 0.726667 0.805195
4 ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU 0.726667 1
5 ASP PHE GLU GLU ILE PRO GLY GLU PTR 0.658228 0.883117
6 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.583851 0.792208
7 SER ILE TYR PHE TPO PRO GLU LEU TYR ASP 0.545977 0.839506
8 PHE GLN PRO GLN ASN GLY GLN PHE ILE 0.525 0.721519
9 PHE GLU ALA ILE PRO ALA GLU TYR LEU 0.52439 0.766234
10 LEU TYR ALA SER PRO GLN LEU GLU GLY PHE 0.514451 0.75
11 TRP ASP ILE PRO PHE 0.514286 0.684211
12 TRP MET ASP PHE ASP ASP ASP ILE PRO PHE 0.514286 0.684211
13 ASN TRP SER HIS PRO GLN PHE GLU LYS 0.509317 0.6375
14 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.505882 0.716049
15 ALA ILE ALA TYR PHE ILE PRO ASP GLN ALA 0.487805 0.766234
16 GLY TYR GLN ASP TYR GLU PRO GLU ALA 0.486842 0.701299
17 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.47486 0.636364
18 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.473054 0.709302
19 ASN GLY TYR GLU ASN PRO THR TYR LYS 0.47093 0.728395
20 PRO GLN PTR GLU PTR ILE PRO ALA 0.467836 0.846154
21 TRP GLU TYR ILE PRO ASN VAL 0.465909 0.743902
22 PRO GLN PTR GLU GLU ILE PRO ILE 0.461988 0.820513
23 GLU GLY GLN PTR GLN PRO GLN PRO ALA 0.461538 0.794872
24 LYS PRO PHE PTR VAL ASN VAL GLU PHE 0.460674 0.825
25 LEU PHE GLY TYR PRO VAL TYR VAL 0.45509 0.766234
26 PHE SER ALA PTR PRO SER GLU GLU ASP 0.454023 0.790123
27 ASN ASP LYS TYR GLU PRO PHE TRP GLU 0.452128 0.703704
28 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.448864 0.779221
29 GLU TYR LEU GLY LEU ASP VAL PRO VAL 0.447059 0.753247
30 LYS LEU PRO ALA GLN PHE TYR ILE LEU 0.446328 0.769231
31 LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.445087 0.766234
32 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.445087 0.701299
33 LEU LEU PHE GLY TYR PRO VAL TYR VAL 0.445087 0.766234
34 TYR GLN PHE GLY PRO ASP PHE PRO ILE ALA 0.445055 0.794872
35 PHE TYR ALA PRO GLU PRO ILE THR SER LEU 0.441341 0.777778
36 ASP ARG VAL TYR ILE HIS PRO PHE 0.439153 0.741176
37 ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.438503 0.72093
38 ACE GLN PM3 GLU GLU ILE PRO 0.433962 0.75641
39 LEU PRO PHE GLU ARG ALA THR ILE MET 0.433155 0.670455
40 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.432927 0.695122
41 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.430851 0.741176
42 LYS PRO ILE VAL GLN TYR ASP ASN PHE 0.428571 0.775
43 LYS LEU TYR GLN ASN PRO THR THR TYR ILE 0.427778 0.753086
44 ALA PRO ALA TRP LEU PHE GLU ALA 0.426966 0.708861
45 PHE ALA PRO GLY PHE PHE PRO TYR LEU 0.426901 0.782051
46 VAL TYR ILE HIS PRO PHE 0.422857 0.725
47 ARG LEU TYR GLN ASN PRO THR THR TYR ILE 0.421622 0.732558
48 PRO PRO THR LEU HIS GLU LEU TYR ASP LEU 0.417989 0.731707
49 SER ASP ILE LEU PHE PRO ALA ASP SER 0.416667 0.7
50 GLU VAL ALA PRO PRO GLU TYR HIS ARG LYS 0.416244 0.697674
51 GLN ASN GLY PTR GLU ASN PRO THR TYR 0.416185 0.743902
52 ARG PRO MET THR PHE LYS GLY ALA LEU 0.414894 0.651685
53 LYS PRO PHE PTR VAL ASN VAL NH2 0.414773 0.8125
54 ILE LEU LYS GLU PRO VAL HIS GLY VAL 0.414365 0.696203
55 PHE ASN PHE PRO GLN ILE THR 0.413174 0.703704
56 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.412429 0.662791
57 TYR LEU GLY GLY PRO ASP PHE PRO THR ILE 0.411765 0.797468
58 SER SER TYR ARG ARG PRO VAL GLY ILE 0.411111 0.709302
59 TYR LEU LYS GLU PRO VAL HIS GLY VAL 0.410811 0.7375
60 SER ASN TRP SER HIS PRO GLN PHE GLU LYS 0.410526 0.635294
61 ARG GLN PHE GLY PRO ASP PHE PRO THR ILE 0.410526 0.717647
62 PHE LYS TPO GLU GLY PRO ASP SER ASP 0.410112 0.769231
63 ILE THR ASP GLN VAL PRO PHE SER VAL 0.410112 0.703704
64 PHE GLU ASP ASN PHE VAL PRO 0.409938 0.721519
65 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.409836 0.678571
66 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.409574 0.709302
67 ARG PRO GLY ASN PHE LEU GLN SER SER PRO 0.409574 0.655172
68 LYS TYR TYR SER ILE ILE PRO HIS SER ILE 0.409091 0.73494
69 TYR TYR SER ILE ILE PRO HIS SER ILE 0.409091 0.73494
70 ILE MET ASP GLN VAL PRO PHE SER VAL 0.40884 0.678571
71 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.404624 0.609756
72 SER SER PHE TYR PRO SEP ALA GLU GLY 0.404624 0.7875
73 DPN PRO DAR ILE NH2 0.403846 0.621951
74 TYR MET PHE PRO ASN ALA PRO TYR LEU 0.403315 0.738095
75 ARG TYR PRO LEU THR PHE GLY TRP CYS PHE 0.402913 0.724138
76 PHE ALA PRO GLY ASN TYR PRO ALA LEU 0.402235 0.765432
77 ALA LEU TRP GLY PHE VAL PRO VAL LEU 0.402174 0.730769
78 GLN TYR PHE MET TPO GLU PTR VAL ALA 0.402174 0.678571
79 LEU PRO PHE GLU ARG ALA THR VAL MET 0.402116 0.659091
80 LEU PRO PHE ASP LYS THR THR ILE MET 0.401099 0.707317
81 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.4 0.647727
82 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.4 0.705882
83 PHE PRO ARG PRO TRP LEU HIS GLY LEU 0.4 0.694118
84 LEU ASN PHE PRO ILE SER PRO 0.4 0.707317
85 THR PRO TYR ASP ILE ASN GLN MET LEU 0.4 0.714286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1D9I; Ligand: 00P; Similar sites found: 34
This union binding pocket(no: 1) in the query (biounit: 1d9i.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PVS 7HP 0.0462 0.40793 1.41844
2 2GMM MAN MAN 0.02928 0.40697 1.98413
3 1FQJ ALF 0.01696 0.4184 2.43056
4 1FQK ALF 0.02852 0.40599 2.43056
5 2POC UD1 0.02711 0.40247 2.43056
6 2XCF BBQ 0.006371 0.41401 3.0303
7 2G30 ALA ALA PHE 0.01625 0.40562 3.10078
8 3ESS 18N 0.01788 0.41899 3.91304
9 1G4U AF3 0.02946 0.40114 4.34783
10 1HE1 AF3 0.03349 0.40145 4.54545
11 4B4Q A2G GAL NAG FUC GAL GLC 0.02087 0.41255 4.63576
12 3NOJ PYR 0.006264 0.45256 5.46218
13 2YY8 MTA 0.0166 0.40545 5.47264
14 3P7G MAN 0.04903 0.4025 5.47945
15 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.0004634 0.44434 6.25
16 2CJU PHX 0.01968 0.4101 7.07965
17 1HPG BOC ALA ALA PRO GLU 0.0002116 0.49701 8.02139
18 4SGA ACE PRO ALA PRO PHE 0.00004752 0.43822 8.83978
19 4F8L AES 0.0267 0.41564 8.96552
20 3HNB 768 0.008445 0.42004 9.43396
21 2OUA AES 0.00002644 0.56095 9.57447
22 3SUD SUE 0.001657 0.42913 9.85222
23 4OVZ P85 0.03213 0.40552 15.9722
24 1FIW PBZ 0.000000000394 0.57198 44.0972
25 5A8Y VBM 0.000004474 0.48771 45.8716
26 1GJC 130 0.0000000001522 0.6471 46.2451
27 1OSS BEN 0.00000000003163 0.56916 47.0852
28 1RTF BEN 0.0000000001225 0.53686 48.0159
29 1SQA UI1 0.000000001182 0.68589 48.5714
30 3N7O N7O 0.000001974 0.52699 48.6726
31 2AIQ BEN 0.00000003965 0.4931 48.9177
32 1IAU ACE ILE GLU PRO ASJ 0.0000006996 0.60019 49.3392
33 1PQ7 ARG 0.000000000008412 0.66419 49.5536
34 4NFE BEN 0.0000001866 0.46347 49.789
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