Receptor
PDB id Resolution Class Description Source Keywords
5KD8 2.3 Å EC: 7.-.-.- BT_4244 METALLOPEPTIDASE IN COMPLEX WITH TN ANTIGEN. BACTEROIDES THETAIOTAOMICRON (STRAIN A/ DSM 2079 / NCTC 10582 / E50 / VPI-5482) O-GLYCOPEPTIDASE PF13402/M60-LIKE O-GLYCAN HYDROLASE. HY
Ref.: RECOGNITION OF PROTEIN-LINKED GLYCANS AS A DETERMIN PEPTIDASE ACTIVITY. PROC. NATL. ACAD. SCI. V. 114 E679 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:906;
A:905;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
NI A:904;
A:903;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
TNR A:902;
Valid;
none;
submit data
308.285 C11 H20 N2 O8 CC(=O...
ZN A:901;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KD8 2.3 Å EC: 7.-.-.- BT_4244 METALLOPEPTIDASE IN COMPLEX WITH TN ANTIGEN. BACTEROIDES THETAIOTAOMICRON (STRAIN A/ DSM 2079 / NCTC 10582 / E50 / VPI-5482) O-GLYCOPEPTIDASE PF13402/M60-LIKE O-GLYCAN HYDROLASE. HY
Ref.: RECOGNITION OF PROTEIN-LINKED GLYCANS AS A DETERMIN PEPTIDASE ACTIVITY. PROC. NATL. ACAD. SCI. V. 114 E679 2017 U.S.A.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5KD8 - TNR C11 H20 N2 O8 CC(=O)N[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5KD8 - TNR C11 H20 N2 O8 CC(=O)N[C@....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 5KD8 - TNR C11 H20 N2 O8 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TNR; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 TNR 1 1
2 3YW 0.683333 0.895833
3 MAG 0.559322 0.84
4 2F8 0.559322 0.84
5 NG1 0.548387 0.741379
6 GN1 0.548387 0.741379
7 ACA SER SER VAL GLY A2G 0.5 0.90566
8 ACE SER SER VAL GLY A2G 0.5 0.886792
9 NAG GAL 0.485714 0.86
10 GAL NAG 0.485714 0.86
11 NAG NGA 0.478873 0.882353
12 NAG A2G 0.478873 0.882353
13 NAG MBG 0.478873 0.826923
14 NAG A2G GAL 0.475 0.882353
15 A2G MBG 0.472222 0.826923
16 MBG A2G 0.472222 0.826923
17 NAG MAN 0.465753 0.862745
18 GYU 0.464789 0.854545
19 57S 0.461538 0.762712
20 NAG GDL 0.458333 0.882353
21 CBS CBS 0.458333 0.882353
22 NDG NAG 0.458333 0.882353
23 CBS 0.458333 0.882353
24 NAG NM9 0.45 0.867925
25 HD4 0.448718 0.762712
26 MA8 0.445946 0.901961
27 NGA GAL 0.445946 0.843137
28 GAL NGA A2G 0.441558 0.882353
29 NAG NAG NAG NAG NDG 0.434211 0.865385
30 NAG NAG NAG NAG NAG 0.434211 0.865385
31 NAG NAG NDG NAG 0.434211 0.865385
32 NAG NAG NAG NAG NAG NAG 0.434211 0.865385
33 NAG NAG NAG NDG 0.434211 0.865385
34 CTO 0.434211 0.865385
35 NAG NAG NDG 0.434211 0.865385
36 NAG NAG NAG NAG NAG NAG NAG NAG 0.434211 0.865385
37 NDG NAG NAG NDG 0.434211 0.865385
38 NDG NAG NAG NAG 0.434211 0.865385
39 NAG NAG 0.434211 0.867925
40 NAG NDG 0.434211 0.867925
41 NDG NAG NAG 0.434211 0.865385
42 NAG MAN BMA 0.43038 0.86
43 LEC 0.428571 0.676923
44 6ZC 0.428571 0.676923
45 NGA 0.42623 0.833333
46 BM3 0.42623 0.833333
47 HSQ 0.42623 0.833333
48 A2G 0.42623 0.833333
49 NDG 0.42623 0.833333
50 NAG 0.42623 0.833333
51 NGA SER GAL 0.425 0.941176
52 NAG MAN MMA 0.425 0.826923
53 A2G SER GAL 0.425 0.941176
54 GAL TNR 0.425 0.941176
55 GAL SER A2G 0.425 0.941176
56 NAG MUB 0.421687 0.849057
57 NAG AMU 0.421687 0.849057
58 A2G GLA FUC 0.419753 0.843137
59 FUC GLA A2G 0.419753 0.843137
60 FUC GAL A2G 0.419753 0.843137
61 A2G GAL FUC 0.419753 0.843137
62 NGA GAL FUC 0.419753 0.843137
63 3QL 0.417722 0.818182
64 GYT 0.417722 0.783333
65 NGA GAL BGC 0.417722 0.86
66 DLD 0.416667 0.766667
67 SNG 0.415385 0.769231
68 NAG MAN MAN 0.409639 0.86
69 THR NGA GAL NAG 0.408602 0.867925
70 AH0 NAG 0.404762 0.789474
71 NAG AMU NAG AMV 0.4 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KD8; Ligand: TNR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5kd8.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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