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Receptor
PDB id Resolution Class Description Source Keywords
3PMA 2.2 Å EC: 3.4.21.5 2.2 ANGSTROM CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN BOVINE AND SUCROSE OCTASULFATE BOS TAURUS PROTEASE THROMBOSIS FIBRINOLYSIS AGONIST HYDROLASE-HYDROINHIBITOR COMPLEX
Ref.: INTERACTION OF THROMBIN WITH SUCROSE OCTASULFATE. BIOCHEMISTRY V. 50 6973 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CIT B:3;
D:4;
 Invalid;
Invalid;
 none;
none;
 submit data
192.124 C6 H8 O7 C(C(=...
NA B:1;
D:2;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
SCR B:248;
D:248;
 Valid;
Valid;
 none;
none;
 submit data
982.802 C12 H22 O35 S8 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PMA 2.2 Å EC: 3.4.21.5 2.2 ANGSTROM CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN BOVINE AND SUCROSE OCTASULFATE BOS TAURUS PROTEASE THROMBOSIS FIBRINOLYSIS AGONIST HYDROLASE-HYDROINHIBITOR COMPLEX
Ref.: INTERACTION OF THROMBIN WITH SUCROSE OCTASULFATE. BIOCHEMISTRY V. 50 6973 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 3PMA - SCR C12 H22 O35 S8 C([C@@H]1[....
70% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 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 ic50 = 6.9 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 - SCR C12 H22 O35 S8 C([C@@H]1[....
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 ic50 = 6.9 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 0ZG C22 H28 N4 O3 S [H]/N=C(/c....
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 - SCR C12 H22 O35 S8 C([C@@H]1[....
56 3BEF - ASN ASP LYS TYR GLU PRO PHE TRP GLU n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SCR; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 SCR 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 3pma.bio3) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 3JQ3 ADP 1.5444
2 6FTB M0E 2.85714
3 3R75 PYR 3.4749
4 1ONI BEZ 10.1449
Pocket No.: 2; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3pma.bio3) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: 112
This union binding pocket(no: 3) in the query (biounit: 3pma.bio3) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 5JPH COA 1.38889
2 2G86 UMP 1.5444
3 2JFN GLU 1.5444
4 5CPZ SIA SIA GAL NGA GAL 1.9305
5 4UA3 COA 2.06186
6 4W4S B29 2.3166
7 5XVH NAP 2.3166
8 3ETG NDP 2.3166
9 3ETG GLU 2.3166
10 6B3A SAM 2.3166
11 4AVB ACO 2.3166
12 4NSQ COA 2.63158
13 4XB4 45D 2.63158
14 4I4Z 2NE 2.7027
15 3WYJ H78 2.7668
16 1CM0 COA 2.97619
17 4H6U ACO 3
18 2YC5 6BC 3.07018
19 5J6A P46 3.0888
20 3LZW NAP 3.0888
21 3LZW FAD 3.0888
22 2CVZ NDP 3.0888
23 1WP4 NDP 3.0888
24 4MUS LY0 3.31754
25 4MUS 2D8 3.31754
26 6EOP F15 3.4749
27 2J07 HDF 3.4749
28 2J07 FAD 3.4749
29 5HH0 COA 3.5
30 2RIF AMP 3.5461
31 5AAV GW5 3.57143
32 1QSR ACO 3.7037
33 1I1D COA 3.72671
34 1I1D 16G 3.72671
35 4R2I ANP 3.80952
36 3QCP FAD 3.861
37 4URL XAM 3.861
38 3IHZ FK5 3.96825
39 4B5P ACO 4
40 5URY PAM 4.10959
41 1DR1 HBI 4.2328
42 1DR1 NAP 4.2328
43 1CDO NAD 4.2471
44 1TIQ COA 4.44444
45 1QSM ACO 4.60526
46 2QIA U20 4.6332
47 2ZPA ACO 4.6332
48 4A34 FUL 4.7619
49 2JDC CAO 4.79452
50 4XOQ F42 4.83092
51 4PVV HO4 5.01931
52 1EYN 2AN 5.01931
53 4KM2 TOP 5.02793
54 4KM2 ATR 5.02793
55 4MUQ LY0 5.09804
56 4MUQ 2D8 5.09804
57 1YYE 196 5.40541
58 3K9U ACO 5.66038
59 2GZM DGL 5.79151
60 3ZUY TCH 5.79151
61 2FZH DH1 5.82524
62 4V3I ASP LEU THR ARG PRO 5.83658
63 1S7G NAD 6.32411
64 4XB2 HSE 6.56371
65 6BR7 BEF 6.76692
66 5XXS COA 6.81818
67 2PQB GG9 6.89655
68 3LLI FAD 6.94981
69 4OEE GNX IDY 7.09677
70 5H86 BCO 7.14286
71 1RF6 GPJ 7.33591
72 1RF6 S3P 7.33591
73 2WCV FUC 7.85714
74 3GWL FAD 9.43396
75 4QC6 30N 9.49721
76 4NES UD1 10.3448
77 6GAS FAD 10.8108
78 4M8E 29V 10.8225
79 1XPJ TLA 11.1111
80 1BOB ACO 11.1969
81 1JGS SAL 12.3188
82 1QMG APX 13.5135
83 1QNF HDF 13.7931
84 1QNF FAD 13.7931
85 1V0C KNC 17.2414
86 1V0C ACO 17.2414
87 1G8K MGD 17.2414
88 3FRH SAH 17.2414
89 3LCV SAM 17.2414
90 1FM9 570 20.6897
91 4R57 ACO 20.6897
92 1RDT 570 20.6897
93 5K9B FMN 20.6897
94 3WHB DCC 22.6804
95 2JFZ DGL 27.5862
96 2JFZ 003 27.5862
97 3ZM6 2GN 27.5862
98 1E5Q NDP 27.5862
99 1K7L 544 27.5862
100 5Y9D FAD 31.0345
101 3O9Z AKG 31.0345
102 3O9Z NAD 31.0345
103 1DNP FAD 31.0345
104 1JZS MRC 31.0345
105 5FKP 6UL 31.0345
106 6HQD SRT 31.0345
107 3G08 FEE 31.0345
108 1NP7 FAD 37.931
109 4G86 BNT 37.931
110 1T36 U 41.3793
111 1N71 COA 44.8276
112 2Q4V ACO 48.2759
Pocket No.: 4; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3pma.bio3) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: 2
This union binding pocket(no: 5) in the query (biounit: 3pma.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
1 4X9D U5P None
2 2F2H XTG 4.2471
Pocket No.: 6; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3pma.bio4) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: 3
This union binding pocket(no: 7) in the query (biounit: 3pma.bio4) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 6BA2 7KM 3.72881
2 3SCM LGN 34.4828
3 1TV5 N8E 44.8276
Pocket No.: 8; Query (leader) PDB : 3PMA; Ligand: SCR; Similar sites found with APoc: 82
This union binding pocket(no: 8) in the query (biounit: 3pma.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 5JNN 6LM None
2 2GFD RDA 1.27119
3 2YNC YNC 1.5444
4 2PO3 T4K 1.9305
5 4B7X NAP 1.9305
6 1DEK DGP 2.07469
7 4ZB6 GDS 2.24215
8 1KQN NAD 2.3166
9 4C2X NHW 2.3166
10 4GKV NAD 2.3166
11 1U72 NDP 2.68817
12 1U72 MTX 2.68817
13 3DST GRG 2.7027
14 4EN4 GT0 2.7027
15 4EN4 ATP 2.7027
16 4EN4 GT1 2.7027
17 2BGM NAJ 2.7027
18 6D28 NEC 2.7027
19 5HGZ ACO 2.88066
20 2PIA FMN 3.0888
21 5HK9 64O 3.0888
22 5D9J 0N8 3.20856
23 3KA2 2NC 3.44828
24 3FSM 2NC 3.44828
25 5EK3 5PK 3.4749
26 4U63 FAD 3.4749
27 5KF9 ACO 3.4749
28 4JNA FAD 3.861
29 2F5Z FAD 3.861
30 3RNM FAD 3.861
31 3EYA FAD 3.861
32 2FT0 ACO 3.861
33 2C43 COA 3.861
34 4XU6 TDA 4.28571
35 1AJQ SPA 4.30622
36 5LS7 ACO 4.37956
37 4CRZ ACO 4.37956
38 4URN NOV 4.44444
39 1FP1 HCC 4.6332
40 1YRE COA 5.07614
41 2B4D COA 5.26316
42 3K1X DBX 5.38462
43 1JQD SAH 5.40541
44 1JQD HSM 5.40541
45 1WWZ ACO 5.66038
46 5BNS 4VM 5.79151
47 3WR7 COA 5.88235
48 4XPL ACO 6.13497
49 4MNS 2AX 6.91824
50 5ZHW DAL DAL 7.45614
51 3KFC 61X 7.90514
52 2WUL GSH 8.47458
53 1BVY FMN 8.49421
54 5OSW DIU 9.26641
55 1ID0 ANP 9.86842
56 3LEO GSH 10.3226
57 3FAL LO2 10.3306
58 3VC1 SAH 10.3448
59 3VC1 GST 10.3448
60 5YJF SAH 10.3448
61 1WY7 SAH 10.3448
62 1JIL 485 10.8108
63 1R27 MGD 12.3552
64 5LWY OLA 13.4454
65 3MDV CL6 13.7931
66 5EXE 5SR 13.7931
67 2YK7 CSF 15.0579
68 5OOH 9ZZ 17.9612
69 5OOH NAP 17.9612
70 3G9E RO7 20.6897
71 3SP6 IL2 24.1379
72 3RMK BML 24.1379
73 1E3I CXF 27.5862
74 6C7D EOJ 31.0345
75 4ZSI GLP 31.0345
76 1W2T SUC GLA 31.0345
77 2IHK CSF 34.4828
78 5ZCO PGV 34.4828
79 5Z84 PGV 34.4828
80 3U3U EAH 34.4828
81 3WLE NAD 34.4828
82 1MWH GTG 41.3793
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