Receptor
PDB id Resolution Class Description Source Keywords
3bf6 2.5 Å EC: 3.4.21.5 THROMBIN:SURAMIN COMPLEX HOMO SAPIENS THROMBIN SURAMIN BLOOD COAGULATION ACUTE PHASE BLOOD COAGULATION CLEAVAGE ON PAIR OF BASIC RESIDUES DISEASE MUGAMMA-CARBOXYGLUTAMIC ACID GLYCOPROTEIN HYDROLASE KRINGLPROTEASE SECRETED SERINE PROTEASE ZYMOGEN
Ref.: STRUCTURAL AND THERMODYNAMIC ANALYSIS OF THROMBIN:S INTERACTION IN SOLUTION AND CRYSTAL PHASES. BIOCHIM.BIOPHYS.ACTA V.1794 873 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PHE PRO ARG I:1;
 Valid;
 none;
 submit data
404.515 n/a O=C(C...
SVR H:301;
 Valid;
 none;
 ic50 = 40 uM
1297.28 C51 H40 N6 O23 S6 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ANM 2.4 Å EC: 3.4.21.5 TERNARY COMPLEX OF AN ORALLY ACTIVE THROMBIN INHIBITOR WITH THROMBIN AND A C-TERMINAL HIRUDIN DERIVED EXO-SIT INHIBITOR HOMO SAPIENS BLOOD CLOTTING
Ref.: ORALLY ACTIVE THROMBIN INHIBITORS. PART 2: OPTIMIZA THE P2-MOIETY BIOORG.MED.CHEM.LETT. V. 16 2648 2006
Members (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1HXF - ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU n/a n/a
2 1C5N Ki = 20 uM ESI C9 H8 I N2 S c1cc2c(cc(....
3 2JH0 Ki = 2 nM 701 C18 H24 Cl N3 O5 S2 C[C@@H](C(....
4 1WBG ic50 = 1 mM L03 C9 H8 Cl N3 S CSc1[nH]c(....
5 1AFE - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
6 3DA9 Kd = 3.1 uM 44U C23 H29 N3 O2 CCCNC(=O)[....
7 2UUJ - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
8 1QHR - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
9 1QJ1 ic50 = 9 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
10 1AE8 - AZL C21 H33 N5 O4 CCOC(=O)N[....
11 1C5L - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
12 4BAO Ki = 4.29 nM MVF C22 H32 N6 O3 [H]/N=C(/c....
13 2JH5 Ki = 367 nM 895 C17 H22 Cl N3 O5 S2 C[C@@H](C(....
14 1HXE - ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU n/a n/a
15 1QJ6 ic50 = 18 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
16 1AWF Ki = 0.97 uM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
17 2GDE ic50 = 5.7 nM SN3 C26 H43 Cl N6 O10 S [H]/N=C(N)....
18 8KME Ki = 8 uM ACE 0BN CHG MLY LEU PRO NH2 n/a n/a
19 1NY2 - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
20 2H9T - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
21 1QJ7 ic50 = 18 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
22 1UMA - IN2 C8 H18 N4 O3 CN(C)C(=O)....
23 2UUK - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
24 1AD8 Ki = 247 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
25 2UUF - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
26 1XMN - SGN IDS SGN IDS SGN n/a n/a
27 2JH6 Ki = 17 nM 894 C17 H24 Cl N3 O5 S2 C[C@@H](C(....
28 2ANM ic50 = 1.8 nM CDO C23 H32 N6 O4 [H]/N=C(/c....
29 1HAH - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
30 3BF6 ic50 = 40 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
31 1WAY ic50 = 400 uM L02 C14 H16 Cl N3 c1cc(ccc1c....
32 7KME Ki = 40 uM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
70% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1YPE Ki = 8 nM UIP C26 H30 N4 O3 CC[C@@H]1[....
2 1YPM Ki = 1.9 uM RA4 C23 H35 N7 O5 [H]/N=C(N)....
3 1YPJ Ki = 95 nM UIB C26 H32 N4 O3 CC[C@@H]1[....
4 1YPG Ki = 10 nM UIR C27 H30 N4 O3 c1cc(ccc1[....
5 1H8D - PHW C45 H48 N3 O9 P CO/C=C/C[C....
6 1H8I - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
7 1YPL Ki = 10.6 uM RA8 C23 H38 N6 O4 S [H]/N=C(/N....
8 3U8T Ki = 16.5 uM DPN PRO DAR CYS NH2 n/a n/a
9 1EB1 Ki = 37 pM ZAL PRO MMO n/a n/a
10 1YPK - CCR C29 H39 N5 O7 S Cc1cc(c(c(....
11 1SB1 Ki = 128 nM 165 C28 H35 N5 O4 S2 c1ccc(cc1)....
12 4LOY - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
13 4HFP Kd = 42 nM 15U C23 H36 N6 O5 S [H]/N=C(N)....
14 1TWX - ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU n/a n/a
15 1VR1 - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
16 3BV9 Ki = 4.4 uM DAR OIC PRO DAL 4PH NH2 n/a n/a
17 3U8R Ki = 7.7 uM DPN PRO DAR ILE NH2 n/a n/a
18 3U8O Ki = 0.92 uM DPN PRO DAR DTH NH2 n/a n/a
19 1ETR - MIT C23 H37 N6 O5 S C[C@@H]1CC....
20 1ETS Ki = 6 nM MID C27 H31 N5 O4 S [H]/N=C(/c....
21 1HXF - ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU n/a n/a
22 1C5N Ki = 20 uM ESI C9 H8 I N2 S c1cc2c(cc(....
23 2JH0 Ki = 2 nM 701 C18 H24 Cl N3 O5 S2 C[C@@H](C(....
24 1WBG ic50 = 1 mM L03 C9 H8 Cl N3 S CSc1[nH]c(....
25 1AFE - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
26 3DA9 Kd = 3.1 uM 44U C23 H29 N3 O2 CCCNC(=O)[....
27 2UUJ - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
28 1QHR - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
29 1QJ1 ic50 = 9 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
30 1AE8 - AZL C21 H33 N5 O4 CCOC(=O)N[....
31 1C5L - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
32 4BAO Ki = 4.29 nM MVF C22 H32 N6 O3 [H]/N=C(/c....
33 2JH5 Ki = 367 nM 895 C17 H22 Cl N3 O5 S2 C[C@@H](C(....
34 1HXE - ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU n/a n/a
35 1QJ6 ic50 = 18 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
36 1AWF Ki = 0.97 uM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
37 2GDE ic50 = 5.7 nM SN3 C26 H43 Cl N6 O10 S [H]/N=C(N)....
38 8KME Ki = 8 uM ACE 0BN CHG MLY LEU PRO NH2 n/a n/a
39 1NY2 - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
40 2H9T - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
41 1QJ7 ic50 = 18 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
42 1UMA - IN2 C8 H18 N4 O3 CN(C)C(=O)....
43 2UUK - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
44 1AD8 Ki = 247 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
45 2UUF - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
46 1XMN - SGN IDS SGN IDS SGN n/a n/a
47 2JH6 Ki = 17 nM 894 C17 H24 Cl N3 O5 S2 C[C@@H](C(....
48 2ANM ic50 = 1.8 nM CDO C23 H32 N6 O4 [H]/N=C(/c....
49 1HAH - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
50 3BF6 ic50 = 40 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
51 1WAY ic50 = 400 uM L02 C14 H16 Cl N3 c1cc(ccc1c....
52 7KME Ki = 40 uM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
53 3PMA - GU4 YYJ n/a n/a
54 3BEF - ASN ASP LYS TYR GLU PRO PHE TRP GLU n/a n/a
50% Homology Family (56)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1YPE Ki = 8 nM UIP C26 H30 N4 O3 CC[C@@H]1[....
2 1YPM Ki = 1.9 uM RA4 C23 H35 N7 O5 [H]/N=C(N)....
3 1YPJ Ki = 95 nM UIB C26 H32 N4 O3 CC[C@@H]1[....
4 1YPG Ki = 10 nM UIR C27 H30 N4 O3 c1cc(ccc1[....
5 1H8D - PHW C45 H48 N3 O9 P CO/C=C/C[C....
6 1H8I - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
7 1YPL Ki = 10.6 uM RA8 C23 H38 N6 O4 S [H]/N=C(/N....
8 3U8T Ki = 16.5 uM DPN PRO DAR CYS NH2 n/a n/a
9 1EB1 Ki = 37 pM ZAL PRO MMO n/a n/a
10 1YPK - CCR C29 H39 N5 O7 S Cc1cc(c(c(....
11 1SB1 Ki = 128 nM 165 C28 H35 N5 O4 S2 c1ccc(cc1)....
12 4LOY - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
13 4HFP Kd = 42 nM 15U C23 H36 N6 O5 S [H]/N=C(N)....
14 1TWX - ASP PHE GLU GLU ILE PRO GLY GLU TYS LEU n/a n/a
15 1VR1 - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
16 3BV9 Ki = 4.4 uM DAR OIC PRO DAL 4PH NH2 n/a n/a
17 3U8R Ki = 7.7 uM DPN PRO DAR ILE NH2 n/a n/a
18 3U8O Ki = 0.92 uM DPN PRO DAR DTH NH2 n/a n/a
19 1UVT Ki = 0.023 uM I48 C20 H22 N3 O3 S Cc1cc(cc(c....
20 1ETT Ki = 1.3 uM 4QQ C22 H28 N4 O3 S [H]/N=C(c1....
21 1ETR - MIT C23 H37 N6 O5 S C[C@@H]1CC....
22 1ETS Ki = 6 nM MID C27 H31 N5 O4 S [H]/N=C(/c....
23 1HXF - ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU n/a n/a
24 1C5N Ki = 20 uM ESI C9 H8 I N2 S c1cc2c(cc(....
25 2JH0 Ki = 2 nM 701 C18 H24 Cl N3 O5 S2 C[C@@H](C(....
26 1WBG ic50 = 1 mM L03 C9 H8 Cl N3 S CSc1[nH]c(....
27 1AFE - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
28 3DA9 Kd = 3.1 uM 44U C23 H29 N3 O2 CCCNC(=O)[....
29 2UUJ - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
30 1QHR - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
31 1QJ1 ic50 = 9 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
32 1AE8 - AZL C21 H33 N5 O4 CCOC(=O)N[....
33 1C5L - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
34 4BAO Ki = 4.29 nM MVF C22 H32 N6 O3 [H]/N=C(/c....
35 2JH5 Ki = 367 nM 895 C17 H22 Cl N3 O5 S2 C[C@@H](C(....
36 1HXE - ASP PHE GLU GLU ILE PRO GLY GLU TYR LEU n/a n/a
37 1QJ6 ic50 = 18 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
38 1AWF Ki = 0.97 uM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
39 2GDE ic50 = 5.7 nM SN3 C26 H43 Cl N6 O10 S [H]/N=C(N)....
40 8KME Ki = 8 uM ACE 0BN CHG MLY LEU PRO NH2 n/a n/a
41 1NY2 - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
42 2H9T - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
43 1QJ7 ic50 = 18 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
44 1UMA - IN2 C8 H18 N4 O3 CN(C)C(=O)....
45 2UUK - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
46 1AD8 Ki = 247 nM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
47 2UUF - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
48 1XMN - SGN IDS SGN IDS SGN n/a n/a
49 2JH6 Ki = 17 nM 894 C17 H24 Cl N3 O5 S2 C[C@@H](C(....
50 2ANM ic50 = 1.8 nM CDO C23 H32 N6 O4 [H]/N=C(/c....
51 1HAH - ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
52 3BF6 ic50 = 40 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
53 1WAY ic50 = 400 uM L02 C14 H16 Cl N3 c1cc(ccc1c....
54 7KME Ki = 40 uM ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU n/a n/a
55 3PMA - GU4 YYJ n/a n/a
56 3BEF - ASN ASP LYS TYR GLU PRO PHE TRP GLU n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PHE PRO ARG; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 PHE PRO ARG 1 1
2 DPN PRO ARG 0.75 0.962963
3 DPN PRO DAR CYS NH2 0.663265 0.945455
4 DPN PRO DAR DTH NH2 0.643564 0.866667
5 DPN PRO DAR ILE NH2 0.643564 0.912281
6 LEU ASP PRO ARG 0.563107 0.819672
7 ARG PRO PRO GLY PHE SER PRO PHE ARG 0.559633 0.912281
8 ARG PRO PRO GLY PHE 0.559633 0.912281
9 0G6 0.534653 0.881356
10 ARG PRO PRO LYS PRO ARG PRO ARG 0.522523 0.909091
11 ACE PRO PRO PRO VAL PRO PRO ARG ARG ARG 0.514286 0.833333
12 PHE ASN ARG PRO VAL 0.508621 0.83871
13 ACE PRO ALA PRO PHE ALA ALA ALA ALA NH2 0.5 0.728814
14 TYR PRO SER LYS PRO ASP ASN PRO GLY GLU 0.495238 0.71875
15 TYR PRO PHE PHE NH2 0.495146 0.737705
16 HIS PRO PHE 0.485437 0.779661
17 MAA LYS PRO PHE 0.477064 0.807018
18 ARG SEP PRO VAL PHE SER 0.473282 0.764706
19 TYR PRO LYS ARG ILE ALA 0.472441 0.8
20 ASP LEU PRO PHE 0.472222 0.737705
21 32U 0.469388 0.890909
22 VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU 0.469027 0.833333
23 GLY PHE ARG PRO 0.46729 0.928571
24 PRO ALA PRO PHE PRO ALA NH2 0.466019 0.807018
25 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.460993 0.764706
26 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.448529 0.8
27 GLU ARG THR ILE PRO ILE THR ARG GLU 0.446281 0.769231
28 ACE PRO PRO PRO VAL IPG PRO ARG ARG 0.439655 0.819672
29 TYR PRO TYR 0.438776 0.737705
30 01B PRO PRO ALA NH2 0.436893 0.714286
31 THR LYS PRO ARG 0.436893 0.909091
32 PHE PRO ARG PRO TRP LEU HIS GLY LEU 0.432258 0.764706
33 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.430769 0.732394
34 LYS ARG ARG ARG HIS PRO SER 0.429688 0.822581
35 MET TRP ARG PRO TRP 0.42963 0.8
36 ASP ARG VAL GLU LEU ASN ALA PRO ARG GLN 0.426357 0.769231
37 06P 0.424242 0.762712
38 P05 0.424242 0.77193
39 ALA PHE ARG ILE PRO LEU THR ARG 0.423358 0.776119
40 TYR MET ASP PHE ASP ASP ASP ILE PRO PHE 0.421569 0.775862
41 ARG ARG LEU PRO ILE PHE SER ARG LEU 0.42029 0.776119
42 PHE SER ALA PTR PRO SER GLU GLU ASP 0.418605 0.643836
43 S49 0.418182 0.694444
44 DMG PRO ARG ARG ARG SER ARG LYS PRO 0.417391 0.735294
45 1IP CYS PHE SER LYS PRO ARG 0.417266 0.776119
46 ARG PRO PRO ILE PHE ILE ARG ARG LEU 0.416058 0.825397
47 ILE ARG ALA ALA PRO PRO PRO LEU PHE 0.416058 0.8125
48 GLY ASP CYS PHE SER LYS PRO ARG 0.414286 0.8125
49 HIS HIS ALA SER PRO ARG LYS 0.413043 0.796875
50 22U 0.411765 0.745763
51 37U 0.411765 0.745763
52 J5K 0.411765 0.725806
53 B03 0.411765 0.77193
54 ARG PRO LYS PRO LEU VAL ASP PRO 0.411765 0.833333
55 LEU PRO PHE ASP ARG THR THR ILE MET 0.410959 0.722222
56 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.410596 0.776119
57 SER PRO LYS ARG ILE ALA 0.408333 0.793651
58 SIN ALA ALA PRO LYS 0.407767 0.77193
59 ASN TRP SER HIS PRO GLN PHE GLU LYS 0.406504 0.707692
60 GOZ 0.405941 0.714286
61 PHE TYR ARG TYR GLY PHE VAL ALA ASN PHE 0.405405 0.655738
62 LEU PRO PHE GLU LEU ARG GLY HIS LEU VAL 0.403974 0.8
63 P97 0.403846 0.6875
64 B01 0.403846 0.709677
65 99P 0.401961 0.758621
66 51U 0.401961 0.785714
67 ACE GLY PHE GLY VAL VAL PRO SER PHE TYR 0.401575 0.692308
68 ARG PRO LYS ARG ILE ALA 0.4 0.819672
69 ARG ARG ARG GLU ARG SER PRO THR ARG 0.4 0.769231
70 ARG THR PHE SER PRO THR TYR GLY LEU 0.4 0.722222
Ligand no: 2; Ligand: SVR; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 SVR 1 1
2 2NG 0.5 0.796875
3 F2H 0.478723 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: PHE PRO ARG; Similar ligands found: 1
No: Ligand Similarity coefficient
1 J3I 0.8822
Ligand no: 2; Ligand: SVR; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ANM; Ligand: CDO; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 2anm.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 1OSS BEN 47.0852
2 1SQA UI1 47.3469
3 1FIW PBZ 49.4163
4 1PQ7 ARG 49.5536
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