Receptor
PDB id Resolution Class Description Source Keywords
4MUS 1.68 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALA-D-AP HOSPHINATE ANALOG ENTEROCOCCUS GALLINARUM CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES CSGIDNATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES NIAIALPHA+BETA PROTEIN METALLOPEPTIDASE HEDGEHOG/DD-PEPTIDASEMEROPS M15B SUBFAMILY ZN2+-DEPENDENT DD-DIPEPTIDASE ZN2+DEPENDENT DD-PENTAPEPTIDASE ANTIBIOTIC RESISTANCE VANCOMRESISTANCE HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE EVOLUTION OF VANCOMYCIN RE D,D-PEPTIDASES. PROC.NATL.ACAD.SCI.USA V. 111 5872 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:201;
A:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
GOL A:205;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
LY0 B:202;
A:203;
Valid;
Valid;
none;
none;
submit data
195.153 C6 H14 N O4 P C[C@@...
2D8 A:202;
B:203;
Valid;
Valid;
none;
none;
submit data
195.153 C6 H14 N O4 P C[C@@...
SO4 A:204;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
CL A:206;
Invalid;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MUS 1.68 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALA-D-AP HOSPHINATE ANALOG ENTEROCOCCUS GALLINARUM CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES CSGIDNATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES NIAIALPHA+BETA PROTEIN METALLOPEPTIDASE HEDGEHOG/DD-PEPTIDASEMEROPS M15B SUBFAMILY ZN2+-DEPENDENT DD-DIPEPTIDASE ZN2+DEPENDENT DD-PENTAPEPTIDASE ANTIBIOTIC RESISTANCE VANCOMRESISTANCE HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE EVOLUTION OF VANCOMYCIN RE D,D-PEPTIDASES. PROC.NATL.ACAD.SCI.USA V. 111 5872 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 4MUS - LY0 C6 H14 N O4 P C[C@@H](C[....
2 4MUT - DAL C3 H7 N O2 C[C@H](C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 4MUS - LY0 C6 H14 N O4 P C[C@@H](C[....
2 4MUT - DAL C3 H7 N O2 C[C@H](C(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 4MUS - LY0 C6 H14 N O4 P C[C@@H](C[....
2 4MUT - DAL C3 H7 N O2 C[C@H](C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LY0; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 2D8 1 1
2 LY0 1 1
3 AEP 0.594595 0.842105
4 P8D 0.552632 0.914286
5 PHY 0.5 0.8
Ligand no: 2; Ligand: 2D8; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 2D8 1 1
2 LY0 1 1
3 AEP 0.594595 0.842105
4 P8D 0.552632 0.914286
5 PHY 0.5 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MUS; Ligand: 2D8; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4mus.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4MUS; Ligand: LY0; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 4mus.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ML1 MGD 0.0318 0.43006 2.8436
2 3PMA SCR 0.001686 0.4626 3.31754
3 4H4D 10E 0.007408 0.40973 3.31754
4 5VKT NAP 0.02232 0.40942 3.31754
5 4WB7 ATP 0.0353 0.40361 3.31754
6 3D3W NAP 0.02761 0.40809 3.79147
7 4M52 M52 0.01123 0.40752 3.79147
8 1PR9 NAP 0.03241 0.40449 3.79147
9 1NJF ADP 0.01025 0.41135 4.73934
10 2Q2V NAD 0.02393 0.4113 5.6872
11 4ETZ C2E 0.006395 0.40685 6.16114
12 5W0N 2KH 0.01352 0.40168 6.16114
13 2DHC DCE 0.005748 0.42557 8.05687
14 1ZBQ NAD 0.01109 0.42729 9.47867
Pocket No.: 3; Query (leader) PDB : 4MUS; Ligand: LY0; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4mus.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4MUS; Ligand: 2D8; Similar sites found: 5
This union binding pocket(no: 4) in the query (biounit: 4mus.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2DHC DCE 0.0105 0.41591 8.05687
2 1ZBQ NAD 0.01704 0.41032 9.47867
3 3LKF PC 0.01387 0.40139 9.47867
4 5E1M PRO PRO LYS ARG ILE ALA 0.02766 0.40216 12.3223
5 5E1M SAH 0.02766 0.40216 12.3223
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