Structure of PDB 7onn Chain A Binding Site BS01

Receptor Information

>7onn Chain A (length=403) Species: 83333 (Escherichia coli K-12)

SRGMITDRSGRPLAVSVPVGGGESRRYYPSGEVTAHLIGFTNVDSQGIEG
VEKSFDKWLTGQAHNLALSIDERLQALVYRELNNAVAFNKAESGSAVLVD
VNTGEVLAMANSPSYNPNNLSGTPKEAMRNRTITDVFEPGSTVKPMVVMT
ALQRGVVRENSVLNTIPYRINGHEIKDVARYSELTLTGVLQKSSNVGVSK
LALAMPSSALVDTYSRFGLGKATNLGLVGERSGLYPQKQRWSDIERATFS
FGYGLMVTPLQLARVYATIGSYGIYRPLSITKVDPPVPGERVFPESIVRT
VVHMMESVALPGGGGVKAAIKGYRIAIKTGTAKKVGPDGRYINKYIAYTA
GVAPASQPRFALVVVINDPQAGKYYGGAVSAPVFGAIMGGVLRTMNIEPD
ALT

Ligand information

• Ligand ID: VL5
• InChI: InChI=1S/C25H34N8O10S2/c1-25(2,33-43-45(38,39)40)19(11-34)31-22(35)20(17-13-44-24(27)30-17)32-42-18(23(36)37)12-41-16-7-5-14(6-8-16)21(26)29-15-4-3-9-28-10-15/h5-8,11,13,15,18-19,28,33H,3-4,9-10,12H2,1-2H3,(H2,26,29)(H2,27,30)(H,31,35)(H,36,37)(H,38,39,40)/b32-20-/t15-,18+,19-/m1/s1
• InChIKey: NFNVPYWCKFTXAX-OOLKDPNPSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)(C(C=O)NC(=O)C(=NOC(COc1ccc(cc1)C(=N)NC2CCCNC2)C(=O)O)c3csc(n3)N)NOS(=O)(=O)O
  CACTVS 3.385: CC(C)(NO[S](O)(=O)=O)[CH](NC(=O)C(=NO[CH](COc1ccc(cc1)C(=N)N[CH]2CCCNC2)C(O)=O)c3csc(N)n3)C=O
  CACTVS 3.385: CC(C)(NO[S](O)(=O)=O)[C@H](NC(=O)C(=N\O[C@@H](COc1ccc(cc1)C(=N)N[C@@H]2CCCNC2)C(O)=O)/c3csc(N)n3)C=O
  OpenEye OEToolkits 2.0.7: [H]/N=C(/c1ccc(cc1)OC[C@@H](C(=O)O)O/N=C(/c2csc(n2)N)\C(=O)N[C@H](C=O)C(C)(C)NOS(=O)(=O)O)\N[C@@H]3CCCNC3
• Formula: C25 H34 N8 O10 S2
• Name: (2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid;
  AIC499 (bound)
• PDB chain: 7onn Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7onn Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria.
• Resolution: 1.92 Å
• Binding residue (original residue number in PDB): E304 G306 S307 V344 S359 N361 F417 G418 Y419 T495 G496 T497 A498 K499 Y540 Y541
• Binding residue (residue number reindexed from 1): E138 G140 S141 V178 S193 N195 F251 G252 Y253 T329 G330 T331 A332 K333 Y374 Y375
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.

Gene Ontology

Molecular Function

• GO:0008658 penicillin binding

External links

• PDB: RCSB:7onn, PDBe:7onn, PDBj:7onn
• PDBsum: 7onn
• PubMed: 34356681
• UniProt: P0AD68|FTSI_ECOLI Peptidoglycan D,D-transpeptidase FtsI (Gene Name=ftsI)