Receptor
PDB id Resolution Class Description Source Keywords
4MUQ 1.36 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE V COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG ENTEROCOCCUS FAECALIS 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 VANCRESISTANCE ANTIBIOTIC RESISTANCE 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
GOL A:305;
A:306;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PE3 A:307;
A:309;
A:308;
A:310;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
634.751 C28 H58 O15 C(COC...
EDO A:304;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
LY0 A:302;
Valid;
none;
submit data
195.153 C6 H14 N O4 P C[C@@...
ZN A:301;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
2D8 A:303;
Valid;
none;
submit data
195.153 C6 H14 N O4 P C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MUQ 1.36 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE V COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG ENTEROCOCCUS FAECALIS 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 VANCRESISTANCE ANTIBIOTIC RESISTANCE HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE EVOLUTION OF VANCOMYCIN RE D,D-PEPTIDASES. PROC.NATL.ACAD.SCI.USA V. 111 5872 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 4MUQ - LY0 C6 H14 N O4 P C[C@@H](C[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 4MUQ - LY0 C6 H14 N O4 P C[C@@H](C[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 4MUQ - LY0 C6 H14 N O4 P 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 : 4MUQ; Ligand: 2D8; Similar sites found: 13
This union binding pocket(no: 1) in the query (biounit: 4muq.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3D3W NAP 0.01883 0.41289 0.819672
2 1YKF NAP 0.02338 0.40473 1.96078
3 2PGJ N1C 0.01617 0.40452 1.96078
4 2ZE7 DST 0.02053 0.40238 1.97628
5 5E1M PRO PRO LYS ARG ILE ALA 0.02098 0.41161 2.48963
6 5E1M SAH 0.02098 0.41161 2.48963
7 4KWD JF2 0.01759 0.40423 3.13725
8 1ZBQ NAD 0.01577 0.41561 3.92157
9 4KP7 NAP 0.03591 0.41114 3.92157
10 2IV2 MGD 0.0231 0.41155 5.09804
11 1NJF AGS 0.01394 0.40444 6
12 4CNK FAD 0.01615 0.42425 7.45098
13 4O0L NDP 0.02922 0.40106 11.2727
Pocket No.: 2; Query (leader) PDB : 4MUQ; Ligand: LY0; Similar sites found: 27
This union binding pocket(no: 2) in the query (biounit: 4muq.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3D3W NAP 0.01491 0.42186 0.819672
2 1PR9 NAP 0.03818 0.4008 0.819672
3 1KEV NDP 0.0239 0.4124 1.56863
4 4ZBA GDS 0.02445 0.40494 1.79372
5 1YKF NAP 0.02295 0.4088 1.96078
6 2PGJ N1C 0.02332 0.40047 1.96078
7 2ZE7 DST 0.0233 0.40335 1.97628
8 1GEG NAD 0.02917 0.40349 2.35294
9 2EWM NAD 0.03362 0.40147 2.40964
10 4H4D 10E 0.008834 0.40613 2.7451
11 2ZAT NAP 0.02418 0.40765 3.13725
12 1ZBQ NAD 0.01373 0.42256 3.92157
13 5MZY 8EZ 0.02544 0.40406 4.43548
14 1G8K MGD 0.01529 0.4466 4.51128
15 5VKT NAP 0.02414 0.40769 4.70588
16 5W0N 2KH 0.01395 0.40103 5.09804
17 3KCC CMP 0.004488 0.42869 5.4902
18 2RH1 CAU 0.01488 0.40164 5.4902
19 4WB7 ATP 0.0413 0.40006 5.88235
20 1NJF ADP 0.007586 0.41768 6
21 1NJF AGS 0.01044 0.41453 6
22 3CV6 HXS 0.03205 0.41063 8.23529
23 3CV6 NAP 0.03079 0.41063 8.23529
24 5UKL SIX 0.02727 0.40125 8.62745
25 4O0L NDP 0.03016 0.4039 11.2727
26 4YAG NAI 0.04993 0.40297 11.3725
27 5ABH YWN 0.02019 0.40047 14.902
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