Structure of PDB 6s1x Chain A Binding Site BS04

Receptor Information
>6s1x Chain A (length=696) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFG
LDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENV
SDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIAR
YGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQ
RGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQK
LLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTR
IYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGT
LKKEGWRPRRTILFASWDAMEFGLLGSTEWAEENSRLLQERGVAYINADS
SIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSP
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHS
VYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVL
RKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFD
KSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGES
FPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand IDKRZ
InChIInChI=1S/C20H25IN4O9/c21-12-3-1-11(2-4-12)17(29)22-10-8-15(26)24-14(19(32)33)7-9-23-20(34)25-13(18(30)31)5-6-16(27)28/h1-4,13-14H,5-10H2,(H,22,29)(H,24,26)(H,27,28)(H,30,31)(H,32,33)(H2,23,25,34)/t13-,14-/m0/s1
InChIKeyGMICYHSMDRPTBB-KBPBESRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)CC[C@H](NC(=O)NCC[C@H](NC(=O)CCNC(=O)c1ccc(I)cc1)C(O)=O)C(O)=O
OpenEye OEToolkits 2.0.7c1cc(ccc1C(=O)NCCC(=O)NC(CCNC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)I
OpenEye OEToolkits 2.0.7c1cc(ccc1C(=O)NCCC(=O)N[C@@H](CCNC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O)I
CACTVS 3.385OC(=O)CC[CH](NC(=O)NCC[CH](NC(=O)CCNC(=O)c1ccc(I)cc1)C(O)=O)C(O)=O
FormulaC20 H25 I N4 O9
Name(2~{S})-2-[[(3~{S})-3-[3-[(4-iodophenyl)carbonylamino]propanoylamino]-4-oxidanyl-4-oxidanylidene-butyl]carbamoylamino]pentanedioic acid
ChEMBLCHEMBL4471968
DrugBank
ZINC
PDB chain6s1x Chain A Residue 820 [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]
PDB6s1x Novel beta- and gamma-Amino Acid-Derived Inhibitors of Prostate-Specific Membrane Antigen.
Resolution1.76 Å
Binding residue
(original residue number in PDB)		R210 N257 M424 L428 E457 R463 D465 G518 R534 R536 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R156 N203 M370 L374 E403 R409 D411 G464 R480 R482 Y498 H499 K645 Y646
Annotation score1
Binding affinityMOAD: ic50=107nM
BindingDB: IC50=107nM
Enzymatic activity
Enzyme Commision number 3.4.17.21: glutamate carboxypeptidase II.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0004181 metallocarboxypeptidase activity
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016805 dipeptidase activity
GO:0046872 metal ion binding
GO:1904492 Ac-Asp-Glu binding
GO:1904493 tetrahydrofolyl-poly(glutamate) polymer binding
Biological Process
GO:0006508 proteolysis
GO:0006760 folic acid-containing compound metabolic process
GO:0035609 C-terminal protein deglutamylation
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6s1x, PDBe:6s1x, PDBj:6s1x
PDBsum6s1x
PubMed32097010
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

[Back to BioLiP]