Receptor
PDB id Resolution Class Description Source Keywords
4Y4V 2.04 Å NON-ENZYME: OTHER STRUCTURE OF HELICOBACTER PYLORI CSD6 IN THE D-ALA-BOUND STA HELICOBACTER PYLORI 26695 CSD6 CELL SHAPE L D-CARBOXYPEPTIDASE HELICOBACTER PYLORIFLAGELLIN PEPTIDOGLYCAN HYDROLASE
Ref.: THE CELL SHAPE-DETERMINING CSD6 PROTEIN FROM HELICO PYLORI CONSTITUTES A NEW FAMILY OF L,D-CARBOXYPEPTI J.BIOL.CHEM. V. 290 25103 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DAL A:402;
A:401;
B:402;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 224 uM
89.093 C3 H7 N O2 C[C@H...
GOL A:403;
B:401;
B:404;
B:403;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4Y4V 2.04 Å NON-ENZYME: OTHER STRUCTURE OF HELICOBACTER PYLORI CSD6 IN THE D-ALA-BOUND STA HELICOBACTER PYLORI 26695 CSD6 CELL SHAPE L D-CARBOXYPEPTIDASE HELICOBACTER PYLORIFLAGELLIN PEPTIDOGLYCAN HYDROLASE
Ref.: THE CELL SHAPE-DETERMINING CSD6 PROTEIN FROM HELICO PYLORI CONSTITUTES A NEW FAMILY OF L,D-CARBOXYPEPTI J.BIOL.CHEM. V. 290 25103 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4Y4V Kd = 224 uM DAL C3 H7 N O2 C[C@H](C(=....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4Y4V Kd = 224 uM DAL C3 H7 N O2 C[C@H](C(=....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4Y4V Kd = 224 uM DAL C3 H7 N O2 C[C@H](C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DAL; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA 1 1
2 DAL 1 1
3 VAL 0.611111 0.882353
4 THR 0.578947 0.789474
5 HGY 0.5625 0.666667
6 ABA 0.526316 0.75
7 DBB 0.526316 0.75
8 LEU 0.5 0.681818
9 ILE 0.5 0.714286
10 VAH 0.434783 0.6
11 NVA 0.434783 0.652174
12 C2N 0.428571 0.636364
13 DCY 0.428571 0.608696
14 CYS 0.428571 0.608696
15 FLA 0.428571 0.636364
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4Y4V; Ligand: DAL; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4y4v.bio1) has 4 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4Y4V; Ligand: DAL; Similar sites found: 53
This union binding pocket(no: 2) in the query (biounit: 4y4v.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2OG7 AHB 0.007031 0.40606 1.17994
2 4D8N 0HM 0.01179 0.43547 1.34529
3 2C77 GNP 0.002572 0.45529 2.35988
4 2Q2Y MKR 0.01199 0.43687 2.35988
5 2Q2Y ADP 0.01245 0.43687 2.35988
6 2WSB NAD 0.03501 0.40206 2.3622
7 2OFW ADX 0.03834 0.42141 2.40385
8 1I9G SAM 0.02212 0.40154 2.5
9 2BME GNP 0.001341 0.47889 2.68817
10 3KN5 ANP 0.03058 0.40074 2.76923
11 2D7C GTP 0.008807 0.4329 2.99401
12 1IMB LIP 0.02144 0.40521 3.2491
13 1G16 GDP 0.02165 0.40166 3.52941
14 5JKG 6LF 0.03994 0.41609 3.53698
15 1KMQ GNP 0.002166 0.46846 3.80435
16 3U7S 017 0.02907 0.40049 4.0404
17 3RAB GNP 0.007524 0.43416 4.14201
18 1OIV GDP 0.006036 0.44843 4.18848
19 2XCU C5P 0.008041 0.40895 4.42478
20 2B8W ALF 5GP 0.00268 0.45861 4.57317
21 1TMT DPN PRO ARG 0.01196 0.43251 4.6332
22 2NYR SVR 0.04329 0.40906 5.16605
23 2CWH NDP 0.01625 0.43782 5.60472
24 2CWH PYC 0.01946 0.43782 5.60472
25 1NVU GTP 0.01345 0.41888 5.60472
26 5F90 GLA GAL 0.006226 0.40458 5.76923
27 4BAS GNP 0.008335 0.42411 6.03015
28 1KSH GDP 0.01213 0.42199 6.57895
29 5BSR AMP 0.03848 0.40307 6.64207
30 3MJY FMN 0.02688 0.40698 6.78466
31 3MJY IJZ 0.02688 0.40698 6.78466
32 5UIU 8CG 0.01904 0.41871 7.12074
33 5I0H ADP BEF 0.003961 0.43948 7.37463
34 5X40 ACP 0.01504 0.42779 7.87671
35 1ZHS NAG NAG BMA MAN MAN 0.01305 0.41233 7.9646
36 4U5X GNP 0.00775 0.4225 8.42697
37 1VG8 GNP 0.001589 0.47497 8.69565
38 1TU3 GNP 0.005572 0.43955 8.77193
39 3C6K SPD 0.03054 0.40312 9.43953
40 3C6K MTA 0.03054 0.40312 9.43953
41 4HAT GNP 0.00447 0.4458 10
42 1GWN GTP 0.01311 0.40672 10.2439
43 1RE0 GDP 0.0256 0.40197 10.3659
44 1ZC3 GNP 0.006607 0.43606 10.6195
45 2GCO GNP 0.004587 0.43505 10.9453
46 4URS C2E 0.01383 0.40869 11.1702
47 1MR3 G3D 0.0155 0.4151 11.5044
48 1CXZ GSP 0.002321 0.46196 11.6279
49 5H56 TYD 0.02934 0.42376 11.7949
50 5H56 ADP 0.02934 0.42376 11.7949
51 3WXM GTP 0.00328 0.45609 12.6844
52 1UM0 FMN 0.007189 0.43444 15.6342
53 5UWT GNP 0.005533 0.43972 39.1304
Pocket No.: 3; Query (leader) PDB : 4Y4V; Ligand: DAL; 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: 4y4v.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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