Structure of PDB 1n6f Chain D Binding Site BS01

Receptor Information

>1n6f Chain D (length=1023) Species: 2303 (Thermoplasma acidophilum)

MPNLLLNPDIHGDRIIFVCCDDLWEHDLKSGSTRKIVSNLGVINNARFFP
DGRKIAIRVMRGSSLNTADLYFYNGENGEIKRITYFSGKSTGRRMFTDVA
GFDPDGNLIISTDAMQPFSSMTCLYRVENDGINFVPLNLGPATHILFADG
RRVIGRNTFELPHWKGYRGGTRGKIWIEVNSGAFKKIVDMSTHVSSPVIV
GHRIYFITDIDGFGQIYSTDLDGKDLRKHTSFTDYYPRHLNTDGRRILFS
KGGSIYIFNPDTEKIEKIEIGDLESPEDRIISIPSKFAEDFSPLDGDLIA
FVSRGQAFIQDVSGTYVLKVPEPLRIRYVRRGGDTKVAFIHGTREGDFLG
IYDYRTGKAEKFEENLGNVFAMGVDRNGKFAVVANDRFEIMTVDLETGKP
TVIERSREAMITDFTISDNSRFIAYGFPLKHGETDGYVMQAIHVYDMEGR
KIFAATTENSHDYAPAFDADSKNLYYLSYRSLDPSPDRVVLNFSFEVVSK
PFVIPLIPGSPNPTKLVPRSMTSEAGEYDLNDMYKRSSPINVDPGDYRMI
IPLESSILIYSVPVHGEFAAYYQGAPEKGVLLKYDVKTRKVTEVKNNLTD
LRLSADRKTVMVRKDDGKIYTFPLEKPEDERTVETDKRPLVSSIHEEFLQ
MYDEAWKLARDNYWNEAVAKEISERIYEKYRNLVPLCKTRYDLSNVIVEM
QGEYRTSHSYEMGGTFTDKDPFRSGRIACDFKLDGDHYVVAKAYAGDYSN
EGEKSPIFEYGIDPTGYLIEDIDGETVGAGSNIYRVLSEKAGTSARIRLS
GKGGDKRDLMIDILDDDRFIRYRSWVEANRRYVHERSKGTIGYIHIPDMG
MMGLNEFYRLFINESSYQGLIVDVRFNGGGFVSQLIIEKLMNKRIGYDNP
RRGTLSPYPTNSVRGKIIAITNEYAGSDGDIFSFSFKKLGLGKLIGTRTW
GGVVGITPKRRLIDGTVLTQPEFAFWFRDAGFGVENYGVDPDVEIEYAPH
DYLSGKDPQIDYAIDALIEELRN

Ligand information

• Ligand ID: DKT
• InChI: InChI=1S/C38H57N7O10/c39-37(40)41-20-10-17-27(33(49)42-28(18-19-31(46)47)34(50)44-30(36(52)53)22-25-13-6-2-7-14-25)43-35(51)32(48)29(21-24-11-4-1-5-12-24)45-38(54)55-23-26-15-8-3-9-16-26/h3,8-9,15-16,24-25,27-30H,1-2,4-7,10-14,17-23H2,(H,42,49)(H,43,51)(H,44,50)(H,45,54)(H,46,47)(H,52,53)(H4,39,40,41)/t27-,28-,29+,30-/m0/s1
• InChIKey: LKCWMWZIRUHWBW-ZXYZSCNASA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C(NC(=O)C(NC(=O)C(NC(=O)C(=O)C(NC(=O)OCc1ccccc1)CC2CCCCC2)CCCNC(=[N@H])N)CCC(=O)O)CC3CCCCC3
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)COC(=O)NC(CC2CCCCC2)C(=O)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](CC3CCCCC3)C(=O)O
  CACTVS 3.341: NC(=N)NCCC[C@H](NC(=O)C(=O)[C@@H](CC1CCCCC1)NC(=O)OCc2ccccc2)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CC3CCCCC3)C(O)=O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)COC(=O)NC(CC2CCCCC2)C(=O)C(=O)NC(CCCNC(=N)N)C(=O)NC(CCC(=O)O)C(=O)NC(CC3CCCCC3)C(=O)O
  CACTVS 3.341: NC(=N)NCCC[CH](NC(=O)C(=O)[CH](CC1CCCCC1)NC(=O)OCc2ccccc2)C(=O)N[CH](CCC(O)=O)C(=O)N[CH](CC3CCCCC3)C(O)=O
• Formula: C38 H57 N7 O10
• Name: 4-[2-(3-BENZYLOXYCARBONYLAMINO-4-CYCLOHEXYL-1-HYDROXY-2-OXO-BUTYLAMINO)-5-GUANIDINO-PENTANOYLAMINO]-4-(1-CARBOXY-2-CYCLOHEXYL-ETHYLCARBAMOYL)-BUTYRIC ACID
• DrugBank: DB01984
• ZINC: ZINC000098208801
• PDB chain: 1n6f Chain D Residue 1214

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1n6f Navigation Inside a Protease: Substrate Selection and Product Exit in the Tricorn Protease from Thermoplasma acidophilum
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): R131 R132 Y609 G916 G917 G918 G964 S965 D966 W988 G993 I994 T995 F1011 F1013
• Binding residue (residue number reindexed from 1): R93 R94 Y571 G878 G879 G880 G926 S927 D928 W950 G955 I956 T957 F973 F975
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H746 G918 S965 D966
• Catalytic site (residue number reindexed from 1): H708 G880 S927 D928
• Enzyme Commision number: 3.4.21.-

Gene Ontology

Molecular Function

• GO:0008236 serine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1n6f, PDBe:1n6f, PDBj:1n6f
• PDBsum: 1n6f
• PubMed: 12470958
• UniProt: P96086|TRI_THEAC Tricorn protease (Gene Name=tri)