Structure of PDB 5hld Chain A Binding Site BS02

Receptor Information

>5hld Chain A (length=649) Species: 83333 (Escherichia coli K-12)

AIVFAVLIAIYGVYLDQKIRSRIDGKVWQLPAAVYGRMVNLEPDMTISKN
EMVKLLEATQYRQVSKMTRPGEFTVQANSIEMIRRPFDFPDSKEGQVRAR
LTFDGDHLATIVNMENNRQFGFFRLDPRLITMISSPNGEQRLFVPRSGFP
DLLVDTLLATETQQLVKNLFLSKANEAYMALIMDARYSKDRILELYMNEV
YLGQSGDNEIRGFPLASLYYFGRPVEELSLDQQALLVGMVLALERRNLVL
RLLYDMLSARPQPAFMQLVRQELQAKLGDKVKDLSGVKIFTTFDSVAQDA
AEKAAVEGIPALKKQRKLSDLETAIVVVDRFSGEVRAMVGGSEPQFAGYN
RAMQARRSIGSLAKPATYLTALSQPKIYRLNTWIADAPIALRQPNGQVWS
PQNDDRRYSESGRVMLVDALTRSMNVPTVNLGMALGLPAVTETWIKLGVP
KDQLHPVPAMLLGALNLTPIEVAQAFQTIASGGNRAPLSALRSVIAEDGK
VLYQSFPQAERAVPAQAAYLTLWTMQQVVQRGTGRQLGAKYPNLHLAGKT
GTTNNNVDTWFAGIDGSTVTITWVGRDNNQPTKLYGASGAMSIYQRYLAN
QTPTPLNLVPPEDIADMGVDYDGNFVCSGGMRILPVWTSDPQSLCQQSE

Ligand information

• Ligand ID: M0E
• InChI: InChI=1S/C69H106N5O34P/c1-30(2)15-14-17-31(3)18-19-33(5)22-25-68(9,10)24-13-12-16-32(4)23-26-96-41(61(90)91)29-98-109(94,95)108-66-56(57(107-67(71)92)69(11,93)58(106-66)59(70)88)105-63-44(73-36(8)77)47(82)54(40(101-63)28-97-64-51(86)48(83)45(80)39(27-75)100-64)103-62-43(72-35(7)76)46(81)53(34(6)99-62)102-65-52(87)49(84)50(85)55(104-65)60(89)74-42-37(78)20-21-38(42)79/h13,15,18,20-21,23-24,34,39-41,43-58,62-66,75,80-87,93H,5,12,14,16-17,19,22,25-29H2,1-4,6-11H3,(H2,70,88)(H2,71,92)(H,72,76)(H,73,77)(H,90,91)(H,94,95)(H2,74,78,79,89)/t34-,39-,40-,41-,43-,44-,45-,46-,47-,48+,49+,50-,51-,52-,53-,54-,55+,56-,57-,58-,62+,63+,64-,65-,66-,69+/m1/s1
• InChIKey: NXPRJQIAIORCGO-ZLPAOQQDSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)OC2C(OC(C(C2O)NC(=O)C)OC3C(C(C(OC3OP(=O)(O)OCC(C(=O)O)OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(=O)N)(C)O)OC(=O)N)COC4C(C(C(C(O4)CO)O)O)O)NC(=O)C)O)OC5C(C(C(C(O5)C(=O)NC6=C(C=CC6=O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](O[C@H]([C@@H]([C@H]2O)NC(=O)C)O[C@@H]3[C@H]([C@]([C@H](O[C@@H]3O[P@@](=O)(O)OC[C@H](C(=O)O)OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(=O)N)(C)O)OC(=O)N)CO[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)NC(=O)C)O)O[C@H]5[C@@H]([C@H]([C@H]([C@H](O5)C(=O)NC6=C(C=CC6=O)O)O)O)O
  CACTVS 3.341: C[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](NC(C)=O)[C@@H](O[C@@H]2CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O[C@H]4[C@H](O[C@H](C(N)=O)[C@@](C)(O)[C@@H]4OC(N)=O)O[P@](O)(=O)OC[C@@H](OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(O)=O)[C@H](NC(C)=O)[C@@H](O)[C@@H]1O[C@@H]5O[C@@H]([C@H](O)[C@H](O)[C@H]5O)C(=O)NC6=C(O)C=CC6=O
  ACDLabs 10.04: O=C(NC1=C(O)C=CC1=O)C6OC(OC2C(O)C(NC(=O)C)C(OC2C)OC4C(OC(OC3C(OC(=O)N)C(O)(C)C(OC3OP(=O)(O)OCC(OC\C=C(/C)CC/C=C/C(C)(C)CCC(=C)/C\C=C(/C)CC\C=C(/C)C)C(=O)O)C(=O)N)C(NC(=O)C)C4O)COC5OC(C(O)C(O)C5O)CO)C(O)C(O)C6O
  CACTVS 3.341: C[CH]1O[CH](O[CH]2[CH](O)[CH](NC(C)=O)[CH](O[CH]2CO[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)O[CH]4[CH](O[CH](C(N)=O)[C](C)(O)[CH]4OC(N)=O)O[P](O)(=O)OC[CH](OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(O)=O)[CH](NC(C)=O)[CH](O)[CH]1O[CH]5O[CH]([CH](O)[CH](O)[CH]5O)C(=O)NC6=C(O)C=CC6=O
• Formula: C69 H106 N5 O34 P
• Name: MOENOMYCIN;
  MOENOMYCIN
• PDB chain: 5hld Chain A Residue 902

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5hld Escherichia coli Penicillin-Binding Protein 1B: Structural Insights into Inhibition.
• Resolution: 2.31 Å
• Binding residue (original residue number in PDB): E233 Q271 K274 N275 E323
• Binding residue (residue number reindexed from 1): E161 Q164 K167 N168 E209
• Annotation score: 1
• Binding affinity: MOAD: ic50=64.3nM

Enzymatic activity

• Enzyme Commision number: 2.4.99.28: peptidoglycan glycosyltransferase.
  3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity
• GO:0008658 penicillin binding
• GO:0008955 peptidoglycan glycosyltransferase activity

Biological Process

• GO:0009252 peptidoglycan biosynthetic process
• GO:0046677 response to antibiotic

Cellular Component

• GO:0009274 peptidoglycan-based cell wall

External links

• PDB: RCSB:5hld, PDBe:5hld, PDBj:5hld
• PDBsum: 5hld
• PubMed: 27899450
• UniProt: P02919|PBPB_ECOLI Penicillin-binding protein 1B (Gene Name=mrcB)