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Receptor
PDB id Resolution Class Description Source Keywords
5D2R 1.9 Å NON-ENZYME: OTHER INHIBITOR BOUND CELL SHAPE DETERMINANT PROTEIN CSD4 FROM HEL PYLORI HELICOBACTER PYLORI MIXED ALPHA BETA SANDWICH CARBOXYPEPTIDASE M14 HYDROLASE-INHIBITOR COMPLEX
Ref.: A BACTERIAL CELL SHAPE-DETERMINING INHIBITOR. ACS CHEM.BIOL. V. 11 981 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IOD A:514;
A:518;
A:519;
A:506;
A:522;
A:515;
A:511;
A:504;
A:510;
A:516;
A:507;
A:513;
A:520;
A:508;
A:512;
A:521;
A:517;
A:505;
A:509;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
126.904 I [I-]
ZN A:501;
A:502;
A:503;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
56W A:523;
Valid;
none;
Ki = 1.5 uM
396.33 C14 H25 N2 O9 P CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5D2R 1.9 Å NON-ENZYME: OTHER INHIBITOR BOUND CELL SHAPE DETERMINANT PROTEIN CSD4 FROM HEL PYLORI HELICOBACTER PYLORI MIXED ALPHA BETA SANDWICH CARBOXYPEPTIDASE M14 HYDROLASE-INHIBITOR COMPLEX
Ref.: A BACTERIAL CELL SHAPE-DETERMINING INHIBITOR. ACS CHEM.BIOL. V. 11 981 2016
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 56W; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 56W 1 1
2 BIX 0.451613 0.863636
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5D2R; Ligand: 56W; Similar sites found with APoc: 61
This union binding pocket(no: 1) in the query (biounit: 5d2r.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4M1U A2G MBG 1.3468
2 2PUZ NIG 1.43198
3 2OVW CBI 1.45985
4 1NSA BEN 1.51899
5 1OJJ GLC GAL 1.74129
6 1OJK GLC BGC 1.74129
7 4UIB GWX 1.9544
8 3WH2 FLC 2.04082
9 6F5W KG1 2.16802
10 4KBA 1QM 2.71903
11 3WUC GLC GAL 2.91971
12 6D61 4AA 3.07692
13 2JIG PD2 3.125
14 5O5Y GLC 3.18907
15 1PCA VAL 3.22581
16 1UMZ BGC BGC XYS BGC XYS GAL 3.23741
17 2Y91 98J 3.39623
18 1Z45 GAL 3.41686
19 2IOY RIP 3.53357
20 5TO8 7FM 3.5461
21 3NNT DQA 3.62319
22 2Z9I GLY ALA THR VAL 3.7037
23 5T9C G3P 3.73134
24 7CPA FVF 3.90879
25 4CPA GLY 3.90879
26 4MPO AMP 3.92157
27 4JD0 1KH 3.98406
28 3BZ3 YAM 3.98551
29 4NST ADP 3.9886
30 5EFQ ADP 4.03458
31 3CMJ SRT 4.55581
32 4D4U FUC GAL NAG 4.7836
33 1IS3 LAT 5.18518
34 3X27 TRP 5.37313
35 4B5W PYR 5.46875
36 3NFZ 3NF 5.50459
37 4A38 BZS 5.6701
38 2BOS GLA GAL 5.88235
39 4LCQ URQ 5.92255
40 5L8L ADP 5.98291
41 3P7G MAN 6.16438
42 4P10 2B8 6.18812
43 2V77 PAY 7.11974
44 3ANY 2A3 7.22433
45 2D6M LBT 7.54717
46 3QMN A3P 7.75194
47 3LMS GLY 8.09062
48 4WES HCA 8.88383
49 1W6O LAT 8.95522
50 1GZW GAL BGC 8.95522
51 1W6P NDG GAL 8.95522
52 2PCU ASP 10.1639
53 2PCU PHE ASN ARG PRO VAL 10.1639
54 2BMR 3NT 10.8247
55 1M3U KPL 10.9848
56 6FOF LAT 11.2245
57 3WUD GLC GAL 13.9706
58 5TVF PUT 20
59 5TVM PUT 20
60 1DTD GLU 21.3115
61 5T7I LAT NAG GAL 23.2258
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