Structure of PDB 8rph Chain D Binding Site BS01

Receptor Information

>8rph Chain D (length=608) Species: 1198452 (Janthinobacterium sp. HH01)

DNKVKVAELVAEALENLGIQHAFGIIGAGNVHLFEAIARRGYTEIVCVHH
EQAACMAVQTYYRTNGRIAAALLTTGAGSTNGVTGVVSAWADSIPCIVIA
GNENSKFTFPENPLRMWGVQGYDSCQMVERVSKYQMRVTKMERAVYELEK
GVHLALEGRPGPTWIEIPMDIQSGRIDPATLEHYVAPPAPDYLTPAVAAQ
VDSVLAALAKAERPVLWLGNGIRLAGGERLLKPLLEKLGSPALVSWAGID
MLDSSHPLVFGRAGVYGQRAANFILQNSDYVLAIGTRLAIPQIGYDLNEL
ARLARIDVVDIDGDEAIKHAKRTQENIVCDARVFIEALLARLNAADAPAI
ASKADWVAKCRAYEEQFPWVGAEHADPEGFINSYRFMERLNGFFKDDQVV
VTDMGTALLSGHQVLRFKEGQRFMTSTGLGEMGYGLPAALGVSFANDRGE
VMCLNCDGGMMMNLQELQTMVHHNLPIKLFIFNNDGYLMIKHTQKSLFKS
DYVGTDRKSGVSCPDFSRLAAAFDIPAYQIRGWDECDATLAKVQAHTGPV
ICEVFMHPQQLFSPKLGVVSRADGTLVSPPLEDLSPLIPRDVLEQAMIGG
MHEKSKTL

Ligand information

• Ligand ID: A1H2A
• InChI: InChI=1S/C16H24N4O10P2S/c1-4-16(23,15(21)22)14-20(8-11-7-18-10(3)19-13(11)17)9(2)12(33-14)5-6-29-32(27,28)30-31(24,25)26/h7,23H,4-6,8H2,1-3H3,(H5-,17,18,19,21,22,24,25,26,27,28)/p+1/t16-/m1/s1
• InChIKey: FMOBPODOIDIUAY-MRXNPFEDSA-O
• SMILES:
  OpenEye OEToolkits 2.0.7: CCC(c1[n+](c(c(s1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)(C(=O)O)O
  CACTVS 3.385: CC[C@](O)(C(O)=O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
  OpenEye OEToolkits 2.0.7: CC[C@@](c1[n+](c(c(s1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)(C(=O)O)O
  CACTVS 3.385: CC[C](O)(C(O)=O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
• Formula: C16 H25 N4 O10 P2 S
• Name: (2~{S})-2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-2-yl]-2-oxidanyl-butanoic acid;
  Ketobutyryl-thiamine diphosphate
• PDB chain: 8rph Chain C Residue 703

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8rph JhE from Janthinobacterium sp. HH01
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): I28 E53
• Binding residue (residue number reindexed from 1): I26 E51
• Annotation score: 1

External links

• PDB: RCSB:8rph, PDBe:8rph, PDBj:8rph
• PDBsum: 8rph
• PubMed: 38874074