Receptor
PDB id Resolution Class Description Source Keywords
5KDU 2 Å NON-ENZYME: OTHER ZMPB METALLOPEPTIDASE IN COMPLEX WITH A2,6-SIALYL T-ANTIGEN CLOSTRIDIUM PERFRINGENS (STRAIN ATCC 1DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / TYPE A) GLYCOPEPTIDASE O-GLYCAN PF13402 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:1109;
A:1111;
A:1110;
A:1112;
A:1105;
A:1107;
A:1104;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
ZN A:1113;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
GAL TNR SIA A:1101;
Valid;
none;
submit data
760.676 n/a O=C([...
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: GAL TNR SIA; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL TNR SIA 1 1
2 SIA NAG GAL GAL 0.743119 0.981481
3 SIA NAG GAL 0.666667 0.981818
4 NAG GAL SIA 0.642857 0.981481
5 SIA GAL NAG SIA 0.632479 0.981481
6 GAL NAG SIA GAL 0.603306 0.981481
7 SIA GAL NAG GAL 0.603306 0.981481
8 GAL SIA 0.601942 0.944444
9 GAL SIA NGA GAL 0.596639 0.962963
10 GAL SER A2G 0.591837 0.907407
11 GAL TNR 0.591837 0.907407
12 A2G SER GAL 0.591837 0.907407
13 NGA SER GAL 0.591837 0.907407
14 BGC GAL NAG SIA GAL 0.578125 0.981481
15 SIA GAL NAG GAL GLC 0.578125 0.981481
16 SIA GAL NAG GAL BGC 0.578125 0.981481
17 SIA GAL NDG SIA 0.565574 0.981818
18 4U0 0.550847 0.925926
19 BGC GAL SIA NGA GAL 0.550388 0.962963
20 GAL NGA GAL BGC SIA 0.550388 0.962963
21 GAL NGA SIA GAL BGC 0.550388 0.962963
22 SIA GAL BGC NGA GAL 0.550388 0.962963
23 4U1 0.546219 0.962963
24 SIA GAL A2G 0.533898 0.962963
25 NGA GAL SIA 0.533898 0.962963
26 GAL NGA GAL SIA 0.532258 0.962963
27 SIA GAL NGA GAL 0.532258 0.962963
28 GAL SIA NGA GAL SIA 0.52 0.962963
29 BGC GAL SIA 0.516667 0.925926
30 GAL BGC SIA 0.516667 0.925926
31 SIA GAL GLC 0.516667 0.925926
32 SIA GAL BGC 0.516667 0.925926
33 GLA GLC SIA 0.516667 0.925926
34 BGC SIA GAL 0.516667 0.925926
35 SIA BGC GAL 0.516667 0.925926
36 SIA NAG 0.508929 0.946429
37 NAG SIA GAL 0.504132 0.962963
38 SIA GAL NAG 0.504132 0.962963
39 NGC GAL NGA POL AZI 0.503759 0.787879
40 BGC GAL SIA SIA GAL NGA 0.496241 0.962963
41 GAL BGC GAL SIA NGA SIA 0.496241 0.962963
42 SIA 2FG 0.495575 0.862069
43 SIA GAL 0.495495 0.925926
44 SIA GAL MAG FUC 0.492308 0.927273
45 SIA 2FG NAG 0.491935 0.896552
46 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.489362 0.963636
47 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.489362 0.963636
48 SIA SIA GAL NGA GAL 0.489051 0.945455
49 Z3Q GAL 5N6 0.488722 0.84127
50 SIA GAL NGA 0.487805 0.962963
51 SIA SIA GAL NGA GAL SIA 0.481752 0.945455
52 SIA GAL NAG FUC 0.480916 0.962963
53 NDG FUC SIA GAL 0.480916 0.962963
54 NAG FUC SIA GAL 0.480916 0.962963
55 FUC NDG GAL SIA 0.480916 0.962963
56 SIA GAL NDG FUC 0.480916 0.962963
57 SIA GLA NAG FUC 0.480916 0.962963
58 SIA GAL NGS 0.476923 0.787879
59 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.475524 0.963636
60 SIA SIA GLA BGC 0.473684 0.945455
61 BGC SIA SIA GAL 0.473684 0.945455
62 A2G THR ALA PRO GLY GLY NAG SIA 0.469512 0.794118
63 GAL BGC SIA NGA 0.466165 0.962963
64 BGC GAL SIA NGA 0.466165 0.962963
65 SIA GAL BGC NGA 0.466165 0.962963
66 SIA CMO 0.465347 0.839286
67 NAG GAL NGC 0.465116 0.962963
68 SLT 0.463415 0.907407
69 BGC GAL SIA NGA GAL SIA 0.462585 0.825397
70 SIA GLA NGS FUC 0.457143 0.787879
71 SIA SIA GAL 0.451613 0.945455
72 4U2 0.451613 0.944444
73 BGC 18C GAL NGA SIA GAL 0.451219 0.870968
74 NGC MBG 0.449153 0.909091
75 5N6 GAL 0.441667 0.927273
76 BGC GAL CEQ SLB NGA GAL SIA SIA 0.43871 0.83871
77 MN0 GAL GLC 0.4375 0.925926
78 SIA GAL SIA GLC NGA 0.431507 0.945455
79 SIA GAL SIA BGC NGA 0.431507 0.945455
80 SIA GAL BGC 16C 0.431373 0.870968
81 MNA 0.427184 0.821429
82 BGC 18C GAL SIA 0.425806 0.870968
83 SIA SIA 0.422414 0.927273
84 SLB SIA 0.422414 0.927273
85 SIA WIA 0.420168 0.896552
86 GAL A2G THR 0.419643 0.925926
87 SIA SIA SIA SLB 0.418803 0.927273
88 SIA SIA SIA SIA SIA SIA SIA 0.418803 0.927273
89 SLB SIA SIA 0.418803 0.927273
90 SLB SIA SIA SIA SIA 0.418803 0.927273
91 SIA SIA SIA 0.413223 0.927273
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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