Receptor
PDB id Resolution Class Description Source Keywords
5E97 1.63 Å EC: 3.2.1.166 GLYCOSIDE HYDROLASE LIGAND STRUCTURE 1 HOMO SAPIENS GLYCOSIDE HYDROLASE LIGAND 1 PROTEIN SUGAR HYDROLASE
Ref.: STRUCTURAL CHARACTERIZATION OF HUMAN HEPARANASE REV INSIGHTS INTO SUBSTRATE RECOGNITION. NAT.STRUCT.MOL.BIOL. V. 22 1016 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:605;
A:607;
A:606;
B:201;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
NAG A:604;
A:601;
A:603;
A:602;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NDG BDP BDP NPO NDG A:608;
Valid;
none;
submit data
895.73 n/a O=[N+...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5L9Z 1.57 Å EC: 3.2.1.166 CRYSTAL STRUCTURE OF HUMAN HEPARANASE NUCLEOPHILE MUTANT (E3 COMPLEX WITH UNREACTED GLUCURONIC ACID CONFIGURED AZIRIDINEJ JB355 HOMO SAPIENS HEPARANASE PROBE GH79 HYDROLASE
Ref.: ACTIVITY-BASED PROBES FOR FUNCTIONAL INTERROGATION RETAINING BETA-GLUCURONIDASES. NAT. CHEM. BIOL. V. 13 867 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5E9B - BDP SGN BDP GNS n/a n/a
2 5E97 - NDG BDP BDP NPO NDG n/a n/a
3 5E9C - IDR SGN 5KV UAP n/a n/a
4 5E98 - BDP GNS BDP NPO n/a n/a
5 5L9Z - GUX C15 H27 N4 O5 C(CCCCN1[C....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5E9B - BDP SGN BDP GNS n/a n/a
2 5E97 - NDG BDP BDP NPO NDG n/a n/a
3 5E9C - IDR SGN 5KV UAP n/a n/a
4 5E98 - BDP GNS BDP NPO n/a n/a
5 5L9Z - GUX C15 H27 N4 O5 C(CCCCN1[C....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5E9B - BDP SGN BDP GNS n/a n/a
2 5E97 - NDG BDP BDP NPO NDG n/a n/a
3 5E9C - IDR SGN 5KV UAP n/a n/a
4 5E98 - BDP GNS BDP NPO n/a n/a
5 5L9Z - GUX C15 H27 N4 O5 C(CCCCN1[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDG BDP BDP NPO NDG; Similar ligands found: 73
No: Ligand ECFP6 Tc MDL keys Tc
1 NDG BDP BDP NPO NDG 1 1
2 GNS BDP GNS BDP GNS BDP NPO 0.762376 0.789474
3 6Y2 0.677083 1
4 GNS BDP GNS IDS GNS BDP NPO 0.669565 0.789474
5 LEC NGA 0.578431 1
6 6ZC 0.557895 0.953125
7 LEC 0.557895 0.953125
8 RCB 0.535354 0.828125
9 NPJ 0.530612 0.828125
10 NAG GCU NAG GCU NAG GCU 5AX 0.527778 0.78125
11 NAG BDP NAG BDP NAG BDP NAG 0.527778 0.78125
12 NAG GCU NAG GCD 0.504202 0.735294
13 GAL A2G NPO 0.490566 0.984375
14 NPO A2G GAL 0.490566 0.984375
15 UMG 0.474138 0.73913
16 NAG NAG NDG 0.47 0.765625
17 NAG NAG NAG 0.47 0.765625
18 NAG NAG NAG NAG NAG NAG NAG NAG 0.47 0.765625
19 NAG NAG NAG NDG 0.47 0.765625
20 NAG NAG NAG NAG 0.47 0.765625
21 NAG NAG NAG NAG NDG NAG 0.47 0.765625
22 NDG NAG NAG NDG 0.47 0.765625
23 NDG NAG NAG 0.47 0.765625
24 NAG NAG NAG NAG NDG 0.47 0.765625
25 NAG NAG NAG NAG NAG NAG 0.47 0.765625
26 NAG NAG NAG NAG NAG 0.47 0.765625
27 NDG NAG NAG NAG 0.47 0.765625
28 CTO 0.47 0.765625
29 NDG NAG NAG NDG NAG 0.47 0.765625
30 NAG AMU NAG AMV 0.464286 0.769231
31 GUM 0.456897 0.73913
32 NGA GAL BGC 0.456311 0.703125
33 A2G MBG 0.454545 0.707692
34 MBG A2G 0.454545 0.707692
35 MAN NAG GAL 0.451923 0.703125
36 GAL NAG MAN 0.451923 0.703125
37 GLA NPO 0.442105 0.796875
38 GAL NPO 0.442105 0.796875
39 PNW 0.442105 0.796875
40 PNG 0.442105 0.796875
41 NBZ GLA 0.442105 0.796875
42 MBE 0.442105 0.796875
43 147 0.442105 0.796875
44 PNA 0.442105 0.796875
45 KHP 0.44086 0.742424
46 NAG GDL 0.43 0.75
47 CBS 0.43 0.75
48 CBS CBS 0.43 0.75
49 NAG NDG 0.43 0.75
50 NAG NAG NGT 0.424779 0.684932
51 NOJ NAG NAG NAG 0.423423 0.724638
52 NOJ NAG NAG 0.423423 0.710145
53 GAL NAG GAL 0.422018 0.681818
54 ASG IDR IDR ASG 0.420168 0.702703
55 NGA GLA GAL BGC 0.419643 0.703125
56 NAA NAA AMI 0.416667 0.670886
57 NAG NAG BMA MAN NAG 0.416 0.720588
58 NAG BMA NAG MAN MAN NAG NAG 0.416 0.765625
59 AO3 0.415254 0.675325
60 DLD 0.414414 0.768116
61 NAG MAN BMA NDG MAN NAG GAL 0.414062 0.765625
62 NAG GAL NAG 0.412844 0.75
63 GLC GAL NAG GAL 0.410714 0.703125
64 MAN NAG 0.41 0.703125
65 NAG NAG NAG NAG NAG NAG NAG 0.408696 0.710145
66 NAG MAN MMA 0.407407 0.707692
67 NAG NAG BMA 0.405405 0.705882
68 NAG NDG BMA 0.405405 0.705882
69 BDP ASG BDP ASG BDP ASG 0.403101 0.666667
70 NAG GAL GAL NAG GAL 0.401786 0.75
71 GAL NAG GAL NAG GAL NAG 0.401786 0.765625
72 NAG GAL GAL NAG 0.401786 0.75
73 NAG GAL BGC 0.4 0.703125
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5L9Z; Ligand: GUX; Similar sites found: 16
This union binding pocket(no: 1) in the query (biounit: 5l9z.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2D24 XYS XYS 0.01998 0.41316 3.3419
2 3AYS CT3 0.02178 0.40437 3.8961
3 3II1 BGC 0.0000216 0.57914 6.49351
4 2VRQ XYP XYP AHR 0.000708 0.45803 6.49351
5 4JIE BMA 0.005757 0.43913 6.49351
6 5BRP PNG 0.01953 0.40458 6.49351
7 4CD6 IFM BMA 0.0006299 0.48811 7.79221
8 3RJY GLC 0.01084 0.43036 9.09091
9 3KB6 LAC 0.005661 0.44066 12.987
10 1VPD TLA 0.01258 0.42174 16.8831
11 1Q8Q MAN MMA 0.02154 0.40984 16.8831
12 3UG4 AHR 0.001296 0.42031 19.2802
13 1GPM CIT 0.02888 0.40389 20.7792
14 3EMZ HXH 0.02766 0.40317 23.3766
15 5L77 GUX 0.000002236 0.55827 29.0488
16 1OFS SUC 0.03479 0.40111 31.25
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