Structure of PDB 4kqq Chain A Binding Site BS01

Receptor Information
>4kqq Chain A (length=520) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLA
AALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEE
FRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRR
GRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLV
IMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFS
MSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSS
NVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKA
ETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVIS
PEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRE
NAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGAL
RLMNVPPDNLPTATEQQQVN
Ligand information
Ligand IDVPP
InChIInChI=1S/C23H29N5O8S/c1-4-27-10-11-28(19(31)18(27)30)22(36)25-13(12-8-6-5-7-9-12)16(29)24-14(20(32)33)17-26-15(21(34)35)23(2,3)37-17/h5-9,13-15,17,26H,4,10-11H2,1-3H3,(H,24,29)(H,25,36)(H,32,33)(H,34,35)/t13-,14+,15+,17+/m1/s1
InChIKeyOKSUEATVFIVTFV-AESZEHBQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCN1CCN(C(=O)N[CH](C(=O)N[CH]([CH]2N[CH](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O
OpenEye OEToolkits 1.7.6CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C@@H]([C@H]3N[C@H](C(S3)(C)C)C(=O)O)C(=O)O
ACDLabs 12.01O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)NC(=O)N3C(=O)C(=O)N(CC)CC3
CACTVS 3.385CCN1CCN(C(=O)N[C@@H](C(=O)N[C@@H]([C@H]2N[C@@H](C(O)=O)C(C)(C)S2)C(O)=O)c3ccccc3)C(=O)C1=O
OpenEye OEToolkits 1.7.6CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC(C3NC(C(S3)(C)C)C(=O)O)C(=O)O
FormulaC23 H29 N5 O8 S
Name(2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid;
(5S)-Penicilloic Acid
ChEMBL
DrugBank
ZINCZINC000098209535
PDB chain4kqq Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4kqq Binding of (5S)-Penicilloic Acid to Penicillin Binding Protein 3.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
S294 V333 S349 Y407 Y409 S485 G486 T487 R489 Y498 Y503 F533 G534 G535
Binding residue
(residue number reindexed from 1)
S244 V283 S299 Y357 Y359 S435 G436 T437 R439 Y448 Y453 F483 G484 G485
Annotation score1
Binding affinityMOAD: ic50=126uM
PDBbind-CN: -logKd/Ki=3.90,IC50=126uM
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0008658 penicillin binding
GO:0008955 peptidoglycan glycosyltransferase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0000917 division septum assembly
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0043093 FtsZ-dependent cytokinesis
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4kqq, PDBe:4kqq, PDBj:4kqq
PDBsum4kqq
PubMed23899657
UniProtG3XD46|FTSI_PSEAE Peptidoglycan D,D-transpeptidase FtsI (Gene Name=ftsI)

[Back to BioLiP]