Receptor
PDB id Resolution Class Description Source Keywords
5KDS 1.6 Å NON-ENZYME: OTHER ZMPB METALLOPEPTIDASE IN COMPLEX WITH AN O-GLYCOPEPTIDE (A2, SIALYLATED CORE-3 PENTAPEPTIDE). BOS TAURUS O-GLYCOPEPTIDASE PF13402/M60-LIKE BOVINE SUBMAXILLARY MUCIGLYCAN HYDROLASE
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
EDO A:1106;
A:1108;
A:1105;
A:1107;
A:1104;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
TLA A:1102;
 Invalid;
 none;
 submit data
150.087 C4 H6 O6 [C@@H...
A2G THR ALA PRO GLY GLY NAG SIA G:101;
 Valid;
 Atoms found LESS than expected: % Diff = 0.013;
 submit data
1083.06 n/a O=C([...
EPE A:1103;
 Invalid;
 none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
ZN A:1101;
 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
5KDS 1.6 Å NON-ENZYME: OTHER ZMPB METALLOPEPTIDASE IN COMPLEX WITH AN O-GLYCOPEPTIDE (A2, SIALYLATED CORE-3 PENTAPEPTIDE). BOS TAURUS O-GLYCOPEPTIDASE PF13402/M60-LIKE BOVINE SUBMAXILLARY MUCIGLYCAN HYDROLASE
Ref.: RECOGNITION OF PROTEIN-LINKED GLYCANS AS A DETERMIN PEPTIDASE ACTIVITY. PROC. NATL. ACAD. SCI. V. 114 E679 2017 U.S.A.
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5KDS - A2G THR ALA PRO GLY GLY NAG SIA n/a n/a
2 5KDU - GAL TNR SIA n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5KDS - A2G THR ALA PRO GLY GLY NAG SIA n/a n/a
2 5KDU - GAL TNR SIA n/a n/a
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5KDS - A2G THR ALA PRO GLY GLY NAG SIA n/a n/a
2 5KDU - GAL TNR SIA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A2G THR ALA PRO GLY GLY NAG SIA; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 A2G THR ALA PRO GLY GLY NAG SIA 1 1
2 SIA GLY PRO ALA THR PRO ALA PRO A2G 0.530055 1
3 SIA NAG GAL GAL 0.469512 0.779412
4 GAL TNR SIA 0.469512 0.794118
5 SIA GAL NAG GAL 0.441176 0.779412
6 GAL NAG SIA GAL 0.441176 0.779412
7 SIA GAL NAG SIA 0.423529 0.779412
8 SIA NAG GAL 0.421687 0.808824
9 SIA GAL NGA 0.418182 0.764706
10 NAG GAL SIA 0.415663 0.779412
11 SIA GAL NAG GAL BGC 0.413408 0.779412
12 BGC GAL NAG SIA GAL 0.413408 0.779412
13 SIA GAL NAG GAL GLC 0.413408 0.779412
14 GAL SIA 0.411765 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KDS; Ligand: A2G THR ALA PRO GLY GLY NAG SIA; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 5kds.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DV8 0LX 0.001411 0.461 1.3308
2 3DWB RDF 0.008609 0.40688 1.69811
3 2WPF WPF 0.04415 0.42256 1.81818
4 2WPF FAD 0.04602 0.42038 1.81818
5 2ZXG S23 0.006889 0.41762 2.07547
6 3TDC 0EU 0.01364 0.44357 2.26415
7 1RM8 BAT 0.001219 0.40602 2.95858
8 4IN9 SER TRP PHE PRO 0.02163 0.40496 3.61446
9 1RL4 BRR 0.005268 0.431 3.7234
10 4DD8 BAT 0.0127 0.41174 3.84615
11 1D8C GLV 0.03032 0.41763 3.87275
12 1M2Z BOG 0.03721 0.4142 3.89105
13 1YP1 LYS ASN LEU 0.001205 0.40635 3.9604
14 3E3U NVC 0.008307 0.40365 4.06091
15 2TCL RO4 0.003103 0.42507 4.14201
16 4DR9 BB2 0.005434 0.40809 4.16667
17 1Q1Y BB2 0.005667 0.4112 4.18848
18 1DIG L37 0.01821 0.40665 4.24837
19 1ATL 0QI 0.003743 0.42501 4.45545
20 3G6N MET ALA SER 0.01647 0.40603 4.71204
21 4M00 SUC 0.003909 0.43459 5.54529
22 3M6P BB2 0.008643 0.40117 5.69948
23 1WS1 BB2 0.004601 0.4113 5.76923
24 1MMQ RRS 0.001156 0.42993 5.88235
25 5KDX GAL TNR 0.00006849 0.53122 6.79245
26 3SVJ 4LI 0.005827 0.4145 6.89655
27 3I6B KDO 0.0193 0.40255 7.22222
28 1LES GLC FRU 0.0135 0.41544 9.61539
29 1R55 097 0.006325 0.42207 9.81308
30 1Q3A NGH 0.00131 0.41332 10.9091
31 3WV1 WHH 0.0003435 0.49903 12.8655
32 5F7Y GLC GAL NAG GAL FUC A2G 0.00989 0.40407 13.3333
33 4WKI 3PW 0.006743 0.41182 13.617
34 4YGM URA 0.01544 0.40792 15.3846
35 4ZW3 4S9 0.01364 0.41378 15.6604
36 4RW3 SHV 0.03327 0.40897 15.894
37 5KD8 TNR 0.00001807 0.47589 43.7736
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