Receptor
PDB id Resolution Class Description Source Keywords
2VGK 2.25 Å EC: 3.4.16.4 CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN ACTINOMADURA SP. CELL WALL BIOGENESIS/DEGRADATION ANTIBIOTIC RESISTANCE PEPTIDOGLYCAN SYNTHESIS PROTEASE SECRETED HYDROLASE CELL SHAPE CARBOXYPEPTIDASE PENICILLIN-BINDING ACTINOMADURA PEPTIDOGLYCAN TRANSPEPTIDASE
Ref.: CRYSTAL STRUCTURES OF COMPLEXES OF BACTERIAL DD-PEPTIDASES WITH PEPTIDOGLYCAN-MIMETIC LIGANDS: THE SUBSTRATE SPECIFICITY PUZZLE. J.MOL.BIOL. V. 381 383 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:610;
A:611;
D:610;
D:611;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
REZ A:500;
B:500;
C:500;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
246.26 C10 H18 N2 O5 C[C@H...
SO4 A:600;
A:601;
A:602;
A:603;
A:604;
B:600;
B:601;
B:602;
B:603;
B:604;
C:600;
C:601;
C:602;
C:603;
C:604;
D:600;
D:601;
D:602;
D:603;
D:604;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VGK 2.25 Å EC: 3.4.16.4 CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN ACTINOMADURA SP. CELL WALL BIOGENESIS/DEGRADATION ANTIBIOTIC RESISTANCE PEPTIDOGLYCAN SYNTHESIS PROTEASE SECRETED HYDROLASE CELL SHAPE CARBOXYPEPTIDASE PENICILLIN-BINDING ACTINOMADURA PEPTIDOGLYCAN TRANSPEPTIDASE
Ref.: CRYSTAL STRUCTURES OF COMPLEXES OF BACTERIAL DD-PEPTIDASES WITH PEPTIDOGLYCAN-MIMETIC LIGANDS: THE SUBSTRATE SPECIFICITY PUZZLE. J.MOL.BIOL. V. 381 383 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2VGK - REZ C10 H18 N2 O5 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 6 families.
1 2VGK - REZ C10 H18 N2 O5 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 5 families.
1 2VGK - REZ C10 H18 N2 O5 C[C@H](C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: REZ; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 REZ 1 1
2 REY 0.517857 0.825
3 NPI 0.511628 0.787879
4 W05 0.491228 0.775
5 I38 0.477273 0.702703
6 MLZ 0.446809 0.609756
7 DLY 0.431818 0.638889
8 LYS 0.422222 0.621622
9 DHH 0.422222 0.735294
10 ALY 0.42 0.810811
11 KKA 0.418182 0.789474
12 REX 0.415385 0.804878
13 API 0.414634 0.757576
14 NLE 0.409091 0.611111
15 26P 0.404255 0.742857
16 ACV 0.403226 0.738095
17 UN1 0.4 0.757576
18 11C 0.4 0.757576
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VGK; Ligand: REZ; Similar sites found: 15
This union binding pocket(no: 1) in the query (biounit: 2vgk.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2EFX NFA 0.008345 0.41309 1.92837
2 2O7B HC4 0.01874 0.40611 2.04499
3 1TB3 FMN 0.02164 0.41633 2.84091
4 4A3U FMN 0.009963 0.42633 3.91061
5 1JSH SIA GAL 0.01212 0.41549 5.95611
6 4DDY DN6 0.000534 0.47893 10.2662
7 4DE0 0JB 0.0005733 0.47429 10.2662
8 3G35 F13 0.001549 0.46902 10.2662
9 3G2Y GF4 0.001338 0.44589 10.2662
10 4DE2 DN3 0.0006544 0.41692 10.2662
11 4UA7 3GK 0.0005097 0.41176 10.2662
12 4UAA 3GK 0.0005146 0.4113 10.2662
13 4DDS 0J7 0.0006927 0.4073 10.2662
14 4DE1 0J6 0.0005628 0.40133 10.2662
15 4KQR VPP 0.01624 0.40942 16.3599
Pocket No.: 2; Query (leader) PDB : 2VGK; Ligand: REZ; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 2vgk.bio3) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EOO CIT 0.008308 0.40172 2.26415
2 1QHO ABD 0.02108 0.41646 5.11247
3 3QDY CBS 0.009975 0.40937 6.99301
4 3QDW NDG 0.01154 0.40548 6.99301
5 4DE3 DN8 0.0002446 0.42907 10.2662
Pocket No.: 3; Query (leader) PDB : 2VGK; Ligand: REZ; Similar sites found: 3
This union binding pocket(no: 3) in the query (biounit: 2vgk.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TLL FMN 0.02675 0.40178 2.04499
2 2H6B 3C4 0.03384 0.40285 3.2
3 2WSB NAD 0.04796 0.40451 3.54331
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