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 250 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 217 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 181 families.
1 5KD8 - TNR C11 H20 N2 O8 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TNR; Similar ligands found: 72
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 MAN NAG 0.492754 0.86
8 NDG NAG 0.486111 0.865385
9 NAG GAL 0.485714 0.86
10 NGA GAL 0.485714 0.86
11 GAL NAG 0.485714 0.86
12 NAG NGA 0.478873 0.882353
13 NAG A2G 0.478873 0.882353
14 NAG MBG 0.478873 0.826923
15 A2G MBG 0.472222 0.826923
16 MBG A2G 0.472222 0.826923
17 GYU 0.464789 0.854545
18 57S 0.461538 0.762712
19 ACE SER SER VAL GLY A2G 0.460674 0.87037
20 CBS CBS 0.458333 0.882353
21 NAG NDG 0.458333 0.882353
22 NAG GDL 0.458333 0.882353
23 CBS 0.458333 0.882353
24 NAG NM9 0.45 0.867925
25 MA8 0.445946 0.901961
26 NDG NAG NAG 0.434211 0.865385
27 NDG NAG NAG NDG NAG 0.434211 0.865385
28 NDG NAG NAG NDG 0.434211 0.865385
29 CTO 0.434211 0.865385
30 NAG NAG NAG NDG 0.434211 0.865385
31 NAG NAG NAG 0.434211 0.865385
32 NAG NAG 0.434211 0.867925
33 NAG NAG NAG NAG NAG NAG NAG NAG 0.434211 0.865385
34 NAG NAG NAG NAG NAG 0.434211 0.865385
35 NDG NAG NAG NAG 0.434211 0.865385
36 NAG NAG NAG NAG NAG NAG 0.434211 0.865385
37 NAG NAG NAG NAG NDG NAG 0.434211 0.865385
38 NAG NAG NAG NAG NDG 0.434211 0.865385
39 NAG NAG NAG NAG 0.434211 0.865385
40 NAG NAG NDG 0.434211 0.865385
41 GAL SER A2G 0.43038 0.901961
42 A2G SER GAL 0.43038 0.901961
43 GAL TNR 0.43038 0.901961
44 NGA SER GAL 0.43038 0.901961
45 6ZC 0.428571 0.676923
46 LEC 0.428571 0.676923
47 BM3 0.42623 0.833333
48 NDG 0.42623 0.833333
49 NAG 0.42623 0.833333
50 A2G 0.42623 0.833333
51 HSQ 0.42623 0.833333
52 NGA 0.42623 0.833333
53 NAG MAN MMA 0.425 0.826923
54 NAG MUB 0.421687 0.849057
55 NAG AMU 0.421687 0.849057
56 A2G GAL FUC 0.419753 0.843137
57 FUC GAL A2G 0.419753 0.843137
58 A2G GLA FUC 0.419753 0.843137
59 NGA GAL FUC 0.419753 0.843137
60 FUC GL0 A2G 0.419753 0.843137
61 FUC GLA A2G 0.419753 0.843137
62 NGA GAL BGC 0.417722 0.86
63 3QL 0.417722 0.818182
64 GYT 0.417722 0.783333
65 DLD 0.416667 0.766667
66 SNG 0.415385 0.769231
67 NAG NGO 0.4125 0.785714
68 NAG MAN MAN 0.409639 0.86
69 NAG MAN BMA 0.409639 0.86
70 AH0 NAG 0.404762 0.789474
71 ACA SER SER VAL GLY A2G 0.401961 0.810345
72 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: 35
This union binding pocket(no: 1) in the query (biounit: 5kd8.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3LXI CAM 0.014 0.4 1.42518
2 5AMC GLY NIY 0.002179 0.42768 1.61002
3 3Q8G PEE 0.03172 0.42811 1.875
4 2W41 ADP 0.01562 0.40297 1.97239
5 2Z7I 742 0.02408 0.44259 2.05882
6 3G4G D71 0.02289 0.4025 2.14669
7 4RHP PEF 0.01764 0.40453 2.55319
8 3ZOK GLY 0.009817 0.42045 2.91005
9 1ATL 0QI 0.008221 0.43054 2.9703
10 5V13 JH3 0.02237 0.40301 3.125
11 3G9E RO7 0.03345 0.41144 3.22004
12 4U0S ADP 0.01357 0.40821 3.48837
13 3ZVS MLI 0.005049 0.4059 3.75
14 4DV8 0LX 0.0009112 0.4969 3.80228
15 5UGW GSH 0.001463 0.46063 4
16 4IN9 SER TRP PHE PRO 0.004134 0.42847 4.21687
17 4WKI 3PW 0.002173 0.40953 4.25532
18 5V4R MGT 0.003992 0.43133 4.32099
19 2ALG DAO 0.006245 0.41856 4.34783
20 4DOE CBK 0.008692 0.40914 4.84211
21 5FPN KYD 0.02658 0.40974 5.18784
22 4B52 RDF 0.007663 0.42065 5.26316
23 2P1C GG3 0.006679 0.44418 5.89744
24 3WCA FPS 0.006237 0.44297 6.84932
25 3N7S 3N7 0.01805 0.40517 6.95652
26 5TVI O8N 0.01383 0.40754 7.6087
27 1KUK PCA LYS TRP 0.007188 0.41975 8.86699
28 2PSM BAM 0.00002849 0.48812 9.09091
29 4YSX E23 0.009587 0.4059 9.61539
30 4ZW3 4S9 0.003373 0.46635 10.9123
31 2VWA PTY 0.01427 0.40403 11.8812
32 3AQT RCO 0.01552 0.40217 13.4694
33 3SVJ 4LI 0.01386 0.41715 17.734
34 4ZGM 32M 0.0007607 0.48131 19.3548
35 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.00001807 0.47589 43.7736
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