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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 253 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 209 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 173 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 with APoc: 32
This union binding pocket(no: 1) in the query (biounit: 4muq.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3D3W NAP 0.819672
2 1KEV NDP 1.56863
3 4ZBA GDS 1.79372
4 1YKF NAP 1.96078
5 2PGJ N1C 1.96078
6 2ZE7 DST 1.97628
7 5E1M PRO PRO LYS ARG ILE ALA 2.48963
8 5E1M SAH 2.48963
9 1U1I NAD 2.7451
10 4KWD JF2 3.13725
11 2ZAT NAP 3.13725
12 4KP7 NAP 3.92157
13 4KP7 1UQ 3.92157
14 1ZBQ NAD 3.92157
15 3DOO SKM 4.31373
16 4D1J DGJ 4.31373
17 6D6W GCU 4.70588
18 3PMA SCR 5.09804
19 2IV2 MGD 5.09804
20 5ZIC BMA Z4Y NAG 5.09804
21 1U7T TDT 5.09804
22 3KCC CMP 5.4902
23 1NJF AGS 6
24 3OJF IMJ 6.27451
25 4CNK FAD 7.45098
26 3FXU TSU 8.23529
27 3FGZ BEF 10.1562
28 3O9Z AKG 10.1961
29 4O0L NDP 11.2727
30 6D50 GCB 14.1176
31 5ZHW DAL DAL 41.6667
32 6A6A DAL 42.2222
Pocket No.: 2; Query (leader) PDB : 4MUQ; Ligand: LY0; Similar sites found with APoc: 46
This union binding pocket(no: 2) in the query (biounit: 4muq.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3D3W NAP 0.819672
2 1PR9 NAP 0.819672
3 1KEV NDP 1.56863
4 4ZBA GDS 1.79372
5 1YKF NAP 1.96078
6 6CI9 NAP 1.96078
7 2PGJ N1C 1.96078
8 2ZE7 DST 1.97628
9 1GEG NAD 2.35294
10 2EWM NAD 2.40964
11 4H4D 10E 2.7451
12 5OJI ISN 2.7451
13 2ZAT NAP 3.13725
14 1VL8 NAP 3.52941
15 2OWZ CIT 3.52941
16 1ZBQ NAD 3.92157
17 4D1J DGJ 4.31373
18 3DOO SKM 4.31373
19 5MZY 8EZ 4.43548
20 6BR7 BEF 4.51128
21 1G8K MGD 4.51128
22 5VKT NAP 4.70588
23 3PMA SCR 5.09804
24 5ZIC BMA Z4Y NAG 5.09804
25 5W0N 2KH 5.09804
26 3LPF Z77 5.09804
27 3KCC CMP 5.4902
28 2RH1 CAU 5.4902
29 1NJF ADP 6
30 1NJF AGS 6
31 3OJF IMJ 6.27451
32 4N9I PCG 6.66667
33 1TV5 FMN 7.84314
34 3FXU TSU 8.23529
35 3CV6 NAP 8.23529
36 3CV6 HXS 8.23529
37 5UKL SIX 8.62745
38 3FGZ BEF 10.1562
39 3O9Z AKG 10.1961
40 1BDB NAD 10.5882
41 4O0L NDP 11.2727
42 4YAG NAI 11.3725
43 6D50 GCB 14.1176
44 5ABH YWN 14.902
45 5ZHW DAL DAL 41.6667
46 6A6A DAL 42.2222
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