Receptor
PDB id Resolution Class Description Source Keywords
4KQR 2.01 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUD AERUGINOSA IN COMPLEX WITH (5S)-PENICILLOIC ACID PSEUDOMONAS AERUGINOSA PENICILLIN-BINDING PROTEINS PIPERACILLIN (5S)-PENICILLOIC CELL WALL BIOSYNTHESIS TRANSPEPTIDASE OUT PERIPLASMIC MEMBIOSYNTHETIC PROTEIN BIOSYNTHETIC PROTEIN-ANTIBIOTIC COMPL
Ref.: BINDING OF (5S)-PENICILLOIC ACID TO PENICILLIN BIND PROTEIN 3. ACS CHEM.BIOL. V. 8 2112 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IMD B:609;
A:609;
A:610;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
69.085 C3 H5 N2 c1c[n...
CL B:604;
B:602;
B:603;
A:603;
A:602;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GOL B:607;
B:606;
A:604;
A:606;
A:608;
A:607;
B:605;
B:608;
A:605;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
VPP B:601;
A:601;
Valid;
Valid;
none;
none;
ic50 = 126 uM
535.57 C23 H29 N5 O8 S CCN1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4KQR 2.01 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUD AERUGINOSA IN COMPLEX WITH (5S)-PENICILLOIC ACID PSEUDOMONAS AERUGINOSA PENICILLIN-BINDING PROTEINS PIPERACILLIN (5S)-PENICILLOIC CELL WALL BIOSYNTHESIS TRANSPEPTIDASE OUT PERIPLASMIC MEMBIOSYNTHETIC PROTEIN BIOSYNTHETIC PROTEIN-ANTIBIOTIC COMPL
Ref.: BINDING OF (5S)-PENICILLOIC ACID TO PENICILLIN BIND PROTEIN 3. ACS CHEM.BIOL. V. 8 2112 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 4KQQ ic50 = 126 uM VPP C23 H29 N5 O8 S CCN1CCN(C(....
2 4KQR ic50 = 126 uM VPP C23 H29 N5 O8 S CCN1CCN(C(....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 4KQQ ic50 = 126 uM VPP C23 H29 N5 O8 S CCN1CCN(C(....
2 4KQR ic50 = 126 uM VPP C23 H29 N5 O8 S CCN1CCN(C(....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 4KQQ ic50 = 126 uM VPP C23 H29 N5 O8 S CCN1CCN(C(....
2 4KQR ic50 = 126 uM VPP C23 H29 N5 O8 S CCN1CCN(C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VPP; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 VPP 1 1
2 ZZ7 0.533333 0.642857
3 PNK 0.442105 0.661972
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KQR; Ligand: VPP; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 4kqr.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1W7F ICT 0.00005392 0.53614 1.9544
2 5K1F IMP 0.01502 0.41382 2.18579
3 2Y91 98J 0.0001555 0.52164 2.26415
4 1I1E DM2 0.002343 0.45298 2.30496
5 3UEC ALA ARG TPO LYS 0.03398 0.40193 2.73973
6 4OFJ HIS 0.01602 0.40606 2.74841
7 5O0X FAD 0.01496 0.40339 3.09278
8 5UJ3 CE4 0.0004306 0.45678 3.10345
9 2B6N ALA PRO THR 0.008228 0.41314 3.23741
10 3IHB GLU 0.009092 0.4241 3.28947
11 2BVE PH5 0.00288 0.43379 3.36134
12 5NE2 DGL 0.000009318 0.58385 3.95683
13 1PIG GLC GLC 0.02365 0.40045 4.03226
14 5KXE 6Y2 0.01147 0.42027 4.11523
15 3NY4 SMX 0.003098 0.42733 4.15094
16 3G2Y GF4 0.000001805 0.63181 4.18251
17 4DE0 0JB 0.0000064 0.57419 4.18251
18 4DE2 DN3 0.00001016 0.56427 4.18251
19 4UAA 3GK 0.000009956 0.55659 4.18251
20 4DDS 0J7 0.00001023 0.55602 4.18251
21 4UA7 3GK 0.00001124 0.55404 4.18251
22 4DE1 0J6 0.00001647 0.53869 4.18251
23 4DE3 DN8 0.00002143 0.53332 4.18251
24 3G35 F13 0.00008553 0.48696 4.18251
25 4DDY DN6 0.00001976 0.4741 4.18251
26 3HUN ZZ7 0.001654 0.45494 5.73951
27 1QSC ACE TYR PRO ILE GLN GLU THR 0.01028 0.40335 6.28272
28 5TG5 JW8 0.0002827 0.50406 6.53061
29 5EOO CIT 0.000001995 0.62076 6.79245
30 2ZD8 MER 0.000236 0.46823 6.79245
31 3HCH RSM 0.01855 0.40045 7.53425
32 2JBH 5GP 0.01588 0.40624 7.55556
33 3FGZ BEF 0.008192 0.44097 7.8125
34 2EFX NFA 0.000516 0.42342 8.26446
35 1JOC ITP 0.00631 0.4259 9.6
36 4JF5 FLC 0.003947 0.42681 10.2881
37 5DTK 5F3 0.0003801 0.48653 10.566
38 2VUZ NAG BMA NAG MAN MAN NAG NAG 0.02461 0.40156 10.8527
39 3QX9 ATP 0.01691 0.41103 13.0435
40 2WGV CIT 0.00004874 0.54796 13.3065
41 2RBK VN4 0.01231 0.41994 15.3257
42 2VGK REZ 0.01624 0.40942 16.3599
43 4K91 SIN 0.003681 0.42099 20.8092
44 3I7V B4P 0.01232 0.40416 24.6269
Pocket No.: 2; Query (leader) PDB : 4KQR; Ligand: VPP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4kqr.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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