Structure of PDB 4kqr Chain B Binding Site BS01

Receptor Information
>4kqr Chain B (length=518) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAA
LGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFR
RFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGR
VIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIM
DVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMS
AALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNV
GISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAET
ATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPE
VASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENA
YRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRL
MNVPPDNLPTATEQQQVN
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 chain4kqr Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4kqr Binding of (5S)-Penicilloic Acid to Penicillin Binding Protein 3.
Resolution2.01 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)
S242 V281 S297 Y355 Y357 S433 G434 T435 R437 Y446 Y451 F481 G482 G483
Annotation score1
Binding affinityMOAD: 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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4kqr, PDBe:4kqr, PDBj:4kqr
PDBsum4kqr
PubMed23899657
UniProtG3XD46|FTSI_PSEAE Peptidoglycan D,D-transpeptidase FtsI (Gene Name=ftsI)

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