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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 510 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 391 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 298 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 with APoc: 72
This union binding pocket(no: 1) in the query (biounit: 4kqr.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5NCB JZ3 1.71149
2 1B7H LYS NLE LYS 1.95035
3 1W7F ICT 1.9544
4 3H4V NAP 2.08333
5 5AE2 FAD 2.12766
6 5K1F IMP 2.18579
7 2Y91 98J 2.26415
8 1I1E DM2 2.30496
9 3UEC ALA ARG TPO LYS 2.73973
10 4OFJ HIS 2.74841
11 5JCA FAD 2.8169
12 4ZEI LAO 3.00601
13 5O0X FAD 3.09278
14 5UJ3 CE4 3.10345
15 2B6N ALA PRO THR 3.23741
16 3IHB GLU 3.28947
17 2BVE PH5 3.36134
18 5NE2 DGL 3.95683
19 2WTN FER 3.98406
20 1PIG GLC GLC 4.03226
21 5KXE 6Y2 4.11523
22 3NY4 SMX 4.15094
23 4DE1 0J6 4.18251
24 4DE3 DN8 4.18251
25 4UAA 3GK 4.18251
26 4DDS 0J7 4.18251
27 4DE0 0JB 4.18251
28 4UA7 3GK 4.18251
29 6BT6 3GK 4.18251
30 4DE2 DN3 4.18251
31 4DDY DN6 4.18251
32 3G2Y GF4 4.18251
33 6BU3 3GK 4.19847
34 6HT0 GQ8 4.51613
35 4FJU GLV 4.5584
36 4FJU NAI 4.5584
37 1PZO CBT 4.56274
38 6AYU MLI 4.89914
39 3VV1 GAL FUC 5
40 2P69 PLP 5.22876
41 4YRY FAD 5.43478
42 3HUN ZZ7 5.73951
43 1QSC ACE TYR PRO ILE GLN GLU THR 6.28272
44 4LO6 SIA GAL 6.31579
45 5TG5 JW8 6.53061
46 4G6I RS3 6.66667
47 5YW5 ADE 6.70391
48 5VKM GAL SIA 6.79012
49 5EOO CIT 6.79245
50 2ZD8 MER 6.79245
51 3TCT 3MI 7.08661
52 1PI5 SM2 7.26257
53 3HCH RSM 7.53425
54 2JBH 5GP 7.55556
55 3FGZ BEF 7.8125
56 5ZA2 NXL 8.19209
57 2EFX NFA 8.26446
58 1PVC ILE SER GLU VAL 8.63787
59 2ED4 FAD 8.72483
60 1YQS BSA 8.88252
61 1JOC ITP 9.6
62 5WHT SIA GAL 10.1449
63 4JF5 FLC 10.2881
64 5QB1 F1C 11.5226
65 3QX9 ATP 13.0435
66 2WGV CIT 13.3065
67 1Z2I NAD 13.6872
68 2RBK VN4 15.3257
69 2VGK REZ 16.3599
70 4K91 SIN 20.8092
71 2UYN 2KT 21.7054
72 3I7V B4P 24.6269
Pocket No.: 2; Query (leader) PDB : 4KQR; Ligand: VPP; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 4kqr.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4P8K 38C 2.70833
2 4P8K FAD 2.70833
3 1I0S FMN 4.73373
4 1I0S NAP 4.73373
5 5AYT L6Y 5.66038
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