Structure of PDB 4kqq Chain B Binding Site BS01

Receptor Information
>4kqq Chain B (length=499) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQD
TKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYP
AGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRVTKNAKPGKTLAL
SIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPN
NRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPG
TLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQ
QVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHA
YAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGV
FRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMV
VVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTATEQQQVN
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 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

[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 Y328 V333 S349 Y409 S485 G486 T487 R489 Y498 Y503 F533 G534 G535
Binding residue
(residue number reindexed from 1)
S223 Y257 V262 S278 Y338 S414 G415 T416 R418 Y427 Y432 F462 G463 G464
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

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]