Receptor
PDB id Resolution Class Description Source Keywords
3PA8 2 Å NON-ENZYME: TOXIN_VIRAL STRUCTURE OF THE C. DIFFICILE TCDB CYSTEINE PROTEASE DOMAIN WITH A PEPTIDE INHIBITOR CLOSTRIDIUM DIFFICILE CLAN CD CYSTEINE PROTEASE PROTEASE TOXIN TOXIN-PEPTIDE INCOMPLEX
Ref.: RATIONAL DESIGN OF INHIBITORS AND ACTIVITY-BASED PR TARGETING CLOSTRIDIUM DIFFICILE VIRULENCE FACTOR TC CHEM.BIOL. V. 17 1201 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
621 A:300;
B:300;
Valid;
Valid;
none;
none;
submit data
331.365 C14 H25 N3 O6 CC(C)...
CA A:255;
Invalid;
none;
submit data
40.078 Ca [Ca+2...
IHP A:257;
B:256;
Valid;
Valid;
none;
none;
submit data
660.035 C6 H18 O24 P6 C1(C(...
NA A:256;
B:255;
Invalid;
Invalid;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PA8 2 Å NON-ENZYME: TOXIN_VIRAL STRUCTURE OF THE C. DIFFICILE TCDB CYSTEINE PROTEASE DOMAIN WITH A PEPTIDE INHIBITOR CLOSTRIDIUM DIFFICILE CLAN CD CYSTEINE PROTEASE PROTEASE TOXIN TOXIN-PEPTIDE INCOMPLEX
Ref.: RATIONAL DESIGN OF INHIBITORS AND ACTIVITY-BASED PR TARGETING CLOSTRIDIUM DIFFICILE VIRULENCE FACTOR TC CHEM.BIOL. V. 17 1201 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 60 families.
1 3PA8 - IHP C6 H18 O24 P6 C1(C(C(C(C....
2 3PEE - IHP C6 H18 O24 P6 C1(C(C(C(C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 families.
1 3PA8 - IHP C6 H18 O24 P6 C1(C(C(C(C....
2 3PEE - IHP C6 H18 O24 P6 C1(C(C(C(C....
3 3HO6 - IHP C6 H18 O24 P6 C1(C(C(C(C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 3PA8 - IHP C6 H18 O24 P6 C1(C(C(C(C....
2 3PEE - IHP C6 H18 O24 P6 C1(C(C(C(C....
3 3HO6 - IHP C6 H18 O24 P6 C1(C(C(C(C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 621; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 621 1 1
Ligand no: 2; Ligand: IHP; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 I6P 1 1
2 IHP 1 1
3 IP5 0.652174 1
4 5MY 0.652174 1
5 I5P 0.652174 1
6 5IP 0.652174 1
7 I0P 0.608696 0.965517
8 I7P 0.6 0.965517
9 I8P 0.6 0.965517
10 2YN 0.6 0.965517
11 I4P 0.571429 1
12 5A2 0.555556 0.8
13 5A3 0.555556 0.8
14 4WZ 0.555556 0.8
15 2IP 0.545455 0.933333
16 4IP 0.538462 0.965517
17 ITP 0.52 0.933333
18 IP2 0.5 0.933333
19 I3S 0.481481 0.933333
20 I3P 0.481481 0.933333
21 I4D 0.48 0.9
22 0EJ 0.46875 0.823529
23 4WY 0.454545 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PA8; Ligand: IHP; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 3pa8.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2EV9 SKM 0.03846 0.40319 None
2 2EV9 NAP 0.03846 0.40319 None
3 1GQG DCD 0.01606 0.40946 3.93701
4 3F5K CE5 0.0337 0.40157 3.93701
5 1XSE NDP 0.03767 0.41145 4.72441
6 4ITU 1HS 0.04899 0.40691 4.72441
7 2OFV 242 0.02272 0.41745 5.51181
8 3RJ5 NAD 0.01844 0.42632 5.90551
Pocket No.: 2; Query (leader) PDB : 3PA8; Ligand: 621; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3pa8.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3PA8; Ligand: IHP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3pa8.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3PA8; Ligand: 621; Similar sites found: 103
This union binding pocket(no: 4) in the query (biounit: 3pa8.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1RC0 KT5 0.04625 0.40049 None
2 3FPF MTA 0.03001 0.41993 1.5748
3 3FPF TNA 0.03001 0.41993 1.5748
4 4ZFL 4NK 0.0286 0.40241 1.7094
5 1ZQ9 SAM 0.007757 0.42653 1.9685
6 5N9X ATP 0.02767 0.4016 1.9685
7 4KCF FMN 0.02152 0.40015 1.9685
8 3AB4 LYS 0.01776 0.40438 2.24719
9 1RHC F42 ACN 0.006949 0.44458 2.3622
10 5XDT MB3 0.02236 0.42094 2.3622
11 2WME NAP 0.01127 0.41825 2.3622
12 1SVK ALF GDP 0.02347 0.41516 2.3622
13 1P9B IMO 0.02317 0.41015 2.3622
14 5KVA SAM 0.02586 0.4047 2.3622
15 4CQM NAP 0.04202 0.40388 2.3622
16 4BMX ADE 0.02289 0.40251 2.39044
17 3RG9 NDP 0.02691 0.41868 2.5
18 3RG9 WRA 0.03042 0.41868 2.5
19 3T4L ZEA 0.01328 0.41274 2.75591
20 3EAU PDN 0.03723 0.41195 2.75591
21 2IV3 UDP 0.01824 0.40932 2.75591
22 1LDN NAD 0.04762 0.40092 2.75591
23 3VGL ANP 0.02152 0.40015 2.75591
24 9LDT NAD 0.04939 0.40006 2.75591
25 5JFT ACE ASP GLU VAL ASP 0QE 0.00006799 0.52586 2.81124
26 3DEK RXD 0.0007297 0.48848 2.81124
27 1RZU ADP 0.003602 0.43213 3.14961
28 1QX4 FAD 0.02742 0.4172 3.14961
29 3H8V ATP 0.01214 0.4166 3.14961
30 1QFY FAD 0.04502 0.40642 3.14961
31 1QFY NAP 0.04502 0.40642 3.14961
32 1GAD NAD 0.03087 0.40628 3.14961
33 4WKB TDI 0.02349 0.4053 3.27869
34 5IBP ACE ASP GLU VAL ASP 0QE 0.0002612 0.54131 3.54331
35 3VPH NAD 0.02752 0.41605 3.54331
36 3MMG GLU THR VAL ARG PHE GLN SER ASP 0.02708 0.40931 3.54331
37 2VAR AMP 0.01512 0.40136 3.54331
38 2VAR ANP 0.02865 0.40082 3.54331
39 4OR7 NAP 0.03741 0.40309 3.63636
40 1CS4 GSP 0.0296 0.40726 3.77358
41 1OFD AKG 0.03689 0.40913 3.93701
42 2A8Y MTA 0.02273 0.40439 3.93701
43 3MVH WFE 0.04449 0.40025 3.93701
44 2B1N LYS ALA SER VAL GLY 0.00989 0.40795 4.06504
45 3ZZL TRP 0.01888 0.40497 4.28571
46 1TAD ALF 0.01841 0.41952 4.33071
47 1TAD GDP 0.01841 0.41952 4.33071
48 4A6D SAM 0.0156 0.41281 4.33071
49 4CNG SAH 0.02547 0.41072 4.33071
50 1F0X FAD 0.04377 0.40993 4.33071
51 3VNM SDD 0.01975 0.40396 4.33071
52 4NKW PLO 0.0225 0.40289 4.33071
53 4Q86 AMP 0.01778 0.40232 4.33071
54 2FR1 NDP 0.04967 0.401 4.33071
55 2W9S NDP 0.03452 0.4037 4.34783
56 4MSG 2C6 0.03896 0.40988 4.60829
57 3T31 DCQ 0.04192 0.42385 4.72441
58 3T31 FAD 0.0398 0.42385 4.72441
59 4E70 N7I 0.03813 0.40503 4.72441
60 2BII MTV 0.02905 0.40355 4.72441
61 1TV5 FMN 0.03929 0.40069 4.72441
62 5O2T GSP 0.02809 0.40713 4.81283
63 5AYV KPL 0.03253 0.41417 5.90551
64 5U3F 7TS 0.01387 0.41715 6.29921
65 1T90 NAD 0.02836 0.41312 6.29921
66 2GAG NAD 0.04083 0.41068 6.29921
67 2YAJ 4HP 0.0163 0.40204 6.29921
68 3KJQ B94 0.0000132 0.55537 6.31579
69 1O44 852 0.02993 0.41812 6.48148
70 1SC3 MLI 0.0001206 0.44051 6.81818
71 2W2X GSP 0.02622 0.40282 7.02703
72 3Q9T FAY 0.02457 0.42283 7.08661
73 2ODE ALF GDP 0.02967 0.40847 7.0922
74 2XTZ GSP 0.01854 0.41524 7.48031
75 4B5P ACO 0.01197 0.42807 7.5
76 5LUB 3Y7 0.000198 0.46117 8.26772
77 5ETJ IM5 0.01995 0.40182 8.26772
78 1I1Q TRP 0.01095 0.40578 9.05512
79 1IY8 NAD 0.0486 0.40044 9.05512
80 4I4Z 2NE 0.03843 0.40485 9.44882
81 3R5J ACE ALA ASP VAL ALA ASA 0.00006767 0.53354 9.82143
82 1QXO FMN 0.03428 0.40255 9.84252
83 1Y8Q ATP 0.03404 0.40134 9.84252
84 3UZO GLU 0.0162 0.41975 10.2362
85 5GK9 ACO 0.01936 0.41704 10.6299
86 4CTA ATP 0.02218 0.41115 10.6299
87 4RSL FAD 0.03886 0.41092 10.6299
88 4HVA 4HV 0.00008506 0.5426 11.0236
89 3N9R TD3 0.01572 0.40051 11.0236
90 3H11 ALA ILE GLU THR ASA 0.00002421 0.54232 11.4173
91 5LKT BCO 0.03371 0.40015 11.4173
92 4IQY AR6 0.03228 0.40114 11.6667
93 2IV2 MGD 0.0207 0.42591 12.2047
94 2IV2 2MD 0.04731 0.40108 12.2047
95 4D79 ATP 0.02222 0.4049 12.5984
96 1WDK NAD 0.01569 0.41755 12.9921
97 1V8K ANP 0.01604 0.40008 13.9024
98 3ZOK NAD 0.03593 0.40757 14.5669
99 4F4S EFO 0.01079 0.4034 15.7895
100 5ITZ GDP 0.02915 0.40347 16.5354
101 1NVM NAD 0.0477 0.40302 18.1102
102 4II2 ATP 0.02536 0.40357 19.2771
103 4LNU GDP 0.02879 0.40226 21.3018
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