Receptor
PDB id Resolution Class Description Source Keywords
1lpk 2.2 Å EC: 3.4.21.6 CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 125. HOMO SAPIENS PROTEIN INHIBITOR COMPLEX BLOOD COAGULATION FACTOR SERINE PROTEINASE HYDROLASE
Ref.: DESIGN AND QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP OF 3-AMIDINOBENZYL-1H-INDOLE-2-CARBOXAMIDES AS POTENT, NONCHIRAL, AND SELECTIVE INHIBITORS OF BLOOD COAGULATION FACTOR XA J.MED.CHEM. V. 45 2749 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:1;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
CBB B:301;
Valid;
none;
Ki = 28 nM
433.546 C25 H31 N5 O2 [H]/N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VH6 1.95 Å EC: 3.4.21.6 STRUCTURE AND PROPERTY BASED DESIGN OF FACTOR XA INHIBITORS: PYRROLIDIN-2-ONES WITH BIARYL P4 MOTIFS HOMO SAPIENS SERINE PROTEASE EGF-LIKE DOMAIN BLOOD COAGULATION POLYMORPHISM GLYCOPROTEIN HYDROXYLATION GAMMA-CARBOXYGLUTAMIC ACID CALCIUM ZYMOGEN COMPLEX PROTEASE HYDROLASE CLEAVAGE ON PAIR OF BASIC RESIDUES
Ref.: STRUCTURE AND PROPERTY BASED DESIGN OF FACTOR XA INHIBITORS: PYRROLIDIN-2-ONES WITH BIARYL P4 MOTIFS. BIOORG.MED.CHEM.LETT. V. 18 23 2008
Members (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2Y82 Ki = 4 nM 930 C24 H23 Cl F N3 O3 S c1cc(cc2c1....
2 1KSN Ki = 0.4 nM FXV C25 H27 N4 O4 C[C@H]([C@....
3 1LPK Ki = 28 nM CBB C25 H31 N5 O2 [H]/N=C(C1....
4 1EZQ Ki = 0.9 nM RPR C27 H30 N4 O3 C[C@H]([C@....
5 2WYG Ki = 2 nM 461 C20 H23 Cl F N3 O3 S2 C[C@H](c1c....
6 2VH0 Ki < 1 nM GSI C22 H25 CL F N5 O3 S2 CN(C)Cc1nc....
7 2BOH Ki = 3 nM IIA C25 H27 Cl N4 O2 S CC(C)N1CCC....
8 2J38 Ki = 47 nM GS5 C19 H22 Cl N3 O5 S2 C[C@@H](C(....
9 1F0R Ki = 22 nM 815 C21 H19 N5 O3 S2 c1cc2c(cc(....
10 2Y7Z Ki = 2 nM C0Z C25 H26 Cl N3 O3 S CN(C)[C@H]....
11 1NFX Ki = 3 nM RDR C22 H21 Cl N4 O4 S2 c1cc(cc2c1....
12 2VH6 Ki = 0.2 nM GSV C23 H22 Cl F N2 O5 S3 CS(=O)(=O)....
13 2Y81 Ki = 2 nM 931 C24 H23 Cl F N3 O3 S c1cc(cc2c1....
14 1NFY Ki = 1.3 nM RTR C20 H19 Cl N4 O3 S2 c1cc(ccc1C....
15 2J4I Ki = 1 nM GSJ C23 H31 Cl N4 O6 S2 CC(C)N(CCN....
16 2UWO Ki = 2 nM 701 C18 H24 Cl N3 O5 S2 C[C@@H](C(....
17 2J2U Ki = 90 nM GSQ C19 H23 Cl N4 O5 S C[C@@H](C(....
18 2Y7X Ki = 1 nM MZA C23 H21 Cl F N3 O3 S c1cc(cc2c1....
19 4Y79 Ki = 11 nM 4O6 C19 H24 Cl N3 O5 S C[C@@H](C(....
20 1LPG Ki = 82 nM IMA C34 H36 N5 O2 C[N+](C)(C....
21 2J94 Ki = 534 nM G15 C17 H21 Cl N6 O5 S2 C[C@@H](C(....
22 2CJI Ki = 6 nM GSK C21 H24 Cl N3 O5 S C[C@@H](C(....
23 1LPZ Ki = 25 nM CMB C25 H22 Cl2 N4 O Cc1cccc2c1....
24 2Y80 Ki = 9 nM 439 C25 H26 Cl N3 O3 S CN(C)[C@@H....
25 2UWL Ki = 4 nM 895 C17 H22 Cl N3 O5 S2 C[C@@H](C(....
26 2WYJ Ki = 1 nM 898 C20 H23 Cl F N3 O3 S2 C[C@@H](c1....
27 2UWP Ki = 154 nM 894 C17 H24 Cl N3 O5 S2 C[C@@H](C(....
28 4Y76 - 4O1 C25 H32 Cl N5 O5 S C[C@@H](C(....
29 2J34 Ki = 15 nM GS6 C19 H22 Cl N3 O5 S2 C[C@@H](C(....
30 1F0S Ki = 18 nM PR2 C19 H17 N5 O3 S2 c1cc2c(cc(....
31 1NFW Ki = 1.1 nM RRR C18 H17 Cl N4 O3 S2 c1cc(sc1C=....
32 2J95 Ki = 4 nM GSX C19 H22 Cl N3 O5 S3 C[C@@H](C(....
70% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2Y82 Ki = 4 nM 930 C24 H23 Cl F N3 O3 S c1cc(cc2c1....
2 1KSN Ki = 0.4 nM FXV C25 H27 N4 O4 C[C@H]([C@....
3 1LPK Ki = 28 nM CBB C25 H31 N5 O2 [H]/N=C(C1....
4 1EZQ Ki = 0.9 nM RPR C27 H30 N4 O3 C[C@H]([C@....
5 2WYG Ki = 2 nM 461 C20 H23 Cl F N3 O3 S2 C[C@H](c1c....
6 2VH0 Ki < 1 nM GSI C22 H25 CL F N5 O3 S2 CN(C)Cc1nc....
7 2BOH Ki = 3 nM IIA C25 H27 Cl N4 O2 S CC(C)N1CCC....
8 2J38 Ki = 47 nM GS5 C19 H22 Cl N3 O5 S2 C[C@@H](C(....
9 1F0R Ki = 22 nM 815 C21 H19 N5 O3 S2 c1cc2c(cc(....
10 2Y7Z Ki = 2 nM C0Z C25 H26 Cl N3 O3 S CN(C)[C@H]....
11 1NFX Ki = 3 nM RDR C22 H21 Cl N4 O4 S2 c1cc(cc2c1....
12 2VH6 Ki = 0.2 nM GSV C23 H22 Cl F N2 O5 S3 CS(=O)(=O)....
13 2Y81 Ki = 2 nM 931 C24 H23 Cl F N3 O3 S c1cc(cc2c1....
14 1NFY Ki = 1.3 nM RTR C20 H19 Cl N4 O3 S2 c1cc(ccc1C....
15 2J4I Ki = 1 nM GSJ C23 H31 Cl N4 O6 S2 CC(C)N(CCN....
16 2UWO Ki = 2 nM 701 C18 H24 Cl N3 O5 S2 C[C@@H](C(....
17 2J2U Ki = 90 nM GSQ C19 H23 Cl N4 O5 S C[C@@H](C(....
18 2Y7X Ki = 1 nM MZA C23 H21 Cl F N3 O3 S c1cc(cc2c1....
19 4Y79 Ki = 11 nM 4O6 C19 H24 Cl N3 O5 S C[C@@H](C(....
20 1LPG Ki = 82 nM IMA C34 H36 N5 O2 C[N+](C)(C....
21 2J94 Ki = 534 nM G15 C17 H21 Cl N6 O5 S2 C[C@@H](C(....
22 2CJI Ki = 6 nM GSK C21 H24 Cl N3 O5 S C[C@@H](C(....
23 1LPZ Ki = 25 nM CMB C25 H22 Cl2 N4 O Cc1cccc2c1....
24 2Y80 Ki = 9 nM 439 C25 H26 Cl N3 O3 S CN(C)[C@@H....
25 2UWL Ki = 4 nM 895 C17 H22 Cl N3 O5 S2 C[C@@H](C(....
26 2WYJ Ki = 1 nM 898 C20 H23 Cl F N3 O3 S2 C[C@@H](c1....
27 2UWP Ki = 154 nM 894 C17 H24 Cl N3 O5 S2 C[C@@H](C(....
28 4Y76 - 4O1 C25 H32 Cl N5 O5 S C[C@@H](C(....
29 2J34 Ki = 15 nM GS6 C19 H22 Cl N3 O5 S2 C[C@@H](C(....
30 1F0S Ki = 18 nM PR2 C19 H17 N5 O3 S2 c1cc2c(cc(....
31 1NFW Ki = 1.1 nM RRR C18 H17 Cl N4 O3 S2 c1cc(sc1C=....
32 2J95 Ki = 4 nM GSX C19 H22 Cl N3 O5 S3 C[C@@H](C(....
33 3K9X ic50 = 4 nM MBM C28 H32 N6 O4 Cc1cc2cc(c....
34 1G2L Ki = 57 nM T87 C29 H31 N7 O3 [H]/N=C(/c....
35 3SW2 ic50 = 13 nM FI1 C28 H29 Cl N4 O5 S c1cc(cc2c1....
36 1XKB Ki = 131 nM 4PP C23 H24 N4 O2 c1cc(cc(c1....
37 1XKA Ki = 131 nM 4PP C23 H24 N4 O2 c1cc(cc(c1....
38 4BTU ic50 = 0.5 nM 6XS C24 H28 Cl2 F N5 O5 S2 CN1CCN(CC1....
39 4BTI ic50 = 0.2 nM 7R9 C26 H32 Cl F2 N5 O6 S2 CN(C)[C@H]....
40 3HPT ic50 = 12 nM YET C23 H28 N6 O3 Cc1cc2cc(c....
41 3ENS ic50 = 8.9 nM ENS C25 H29 Cl N6 O4 COC(=O)C(=....
42 1WU1 ic50 = 18 nM D91 C26 H27 Cl N6 O3 S CC(C)C[C@@....
43 4A7I Ki = 0.002 uM A7I C15 H24 Cl N3 O3 S2 CC(C)N1CCC....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2Y82 Ki = 4 nM 930 C24 H23 Cl F N3 O3 S c1cc(cc2c1....
2 1KSN Ki = 0.4 nM FXV C25 H27 N4 O4 C[C@H]([C@....
3 1LPK Ki = 28 nM CBB C25 H31 N5 O2 [H]/N=C(C1....
4 1EZQ Ki = 0.9 nM RPR C27 H30 N4 O3 C[C@H]([C@....
5 2WYG Ki = 2 nM 461 C20 H23 Cl F N3 O3 S2 C[C@H](c1c....
6 2VH0 Ki < 1 nM GSI C22 H25 CL F N5 O3 S2 CN(C)Cc1nc....
7 2J2U Ki = 90 nM GSQ C19 H23 Cl N4 O5 S C[C@@H](C(....
8 2Y7X Ki = 1 nM MZA C23 H21 Cl F N3 O3 S c1cc(cc2c1....
9 4Y79 Ki = 11 nM 4O6 C19 H24 Cl N3 O5 S C[C@@H](C(....
10 1LPG Ki = 82 nM IMA C34 H36 N5 O2 C[N+](C)(C....
11 2J94 Ki = 534 nM G15 C17 H21 Cl N6 O5 S2 C[C@@H](C(....
12 2CJI Ki = 6 nM GSK C21 H24 Cl N3 O5 S C[C@@H](C(....
13 1LPZ Ki = 25 nM CMB C25 H22 Cl2 N4 O Cc1cccc2c1....
14 1NFU Ki = 18 nM RRP C20 H19 Cl N4 O3 S2 c1cc(cc(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CBB; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 CBB 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VH6; Ligand: GSV; Similar sites found: 35
This union binding pocket(no: 1) in the query (biounit: 2vh6.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GL0 ADN 0.01578 0.41587 1.79641
2 3P7G MAN 0.02353 0.41478 2.73973
3 4F8L AES 0.01263 0.427 2.98507
4 4ISS TAR 0.03353 0.4002 2.98507
5 1GPM AMP 0.0003254 0.52407 4.47761
6 3SUD SUE 0.006729 0.40958 5.22388
7 4A7W GTP 0.02695 0.40844 5.97015
8 4DN8 BMA 0.04497 0.40032 5.97015
9 1UI0 URA 0.02183 0.40454 6.82927
10 2YY8 MTA 0.006922 0.42067 6.96517
11 2FKA BEF 0.02072 0.41268 6.97674
12 1QO0 BMD 0.02991 0.40666 7.14286
13 4WCX MET 0.01703 0.41456 7.46269
14 1X8X TYR 0.01847 0.40397 8.95522
15 2W5P CL8 0.001689 0.466 9.70149
16 2CJU PHX 0.01249 0.41776 9.73451
17 2OUA AES 0.0002235 0.50934 12.234
18 1FQJ ALF 0.0192 0.41295 12.6866
19 1HPG BOC ALA ALA PRO GLU 0.001194 0.45718 13.369
20 2XYA 7L4 0.0007612 0.49164 15.9341
21 3QDV NDG 0.03475 0.40725 16.0839
22 5A8Y VBM 0.000001754 0.52052 44.0367
23 1GJC 130 0.0000000001276 0.62882 45.8498
24 2PKA BEN 0.00000001109 0.50637 46.25
25 1RTF BEN 0.00000000003422 0.57436 47.619
26 2AIQ BEN 0.000000006577 0.74477 48.0519
27 1SQA UI1 0.00000000009876 0.7485 48.1633
28 4NFE BEN 0.00000002594 0.4975 48.5232
29 1O5E 132 0.0000000003201 0.61985 48.8189
30 1ELE 0QN 0.0001079 0.4624 49.1667
31 2ZA5 2FF 0.0000000013 0.67909 49.3878
32 3N7O N7O 0.000002421 0.51049 49.5575
33 5WB6 9ZM 0.000000002421 0.6736 49.5902
34 5Q0F 9FA 0.000000009094 0.61037 49.5902
35 1IAU ACE ILE GLU PRO ASJ 0.00000571 0.55354 49.7797
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