Structure of PDB 4ixu Chain C Binding Site BS03

Receptor Information

>4ixu Chain C (length=306) Species: 9606 (Homo sapiens)

HSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSF
TPVPKDDLYNNLIVNPRSVGLANQELAEVVSRAVSDGYSCVTLGGDHSLA
IGTISGHARHCPDLCVVWVDAHADINTPLTTSSGNLHGQPVSFLLRELQD
KVPQLPGFSWIKPCISSASIVYIGLRDVDPPEHFILKNYDIQYFSMRDID
RLGIQKVMERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTY
REGMYIAEEIHNTGLLSALDLVEVNPQLATSEEEAKTTANLAVDVIASSF
GQTREG

Ligand information

• Ligand ID: 38I
• InChI: InChI=1S/C20H30BCl2N2O5/c22-17-6-3-13(9-18(17)23)12-25-15-4-5-16(25)11-14(10-15)20(24,19(26)27)7-1-2-8-21(28,29)30/h3,6,9,14-16,28-30H,1-2,4-5,7-8,10-12,24H2,(H,26,27)/q-1/t14-,15+,16-,20-/m1/s1
• InChIKey: KCKQBVVBSIZAMB-UIVXKWKOSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: [B-](CCCCC(C1CC2CCC(C1)N2Cc3ccc(c(c3)Cl)Cl)(C(=O)O)N)(O)(O)O
  CACTVS 3.370: N[C@](CCCC[B-](O)(O)O)(C1C[C@H]2CC[C@@H](C1)N2Cc3ccc(Cl)c(Cl)c3)C(O)=O
  ACDLabs 12.01: O=C(O)C(N)(C2CC3N(Cc1ccc(Cl)c(Cl)c1)C(C2)CC3)CCCC[B-](O)(O)O
  OpenEye OEToolkits 1.7.6: [B-](CCCC[C@@](C1C[C@H]2CC[C@@H](C1)N2Cc3ccc(c(c3)Cl)Cl)(C(=O)O)N)(O)(O)O
  CACTVS 3.370: N[C](CCCC[B-](O)(O)O)(C1C[CH]2CC[CH](C1)N2Cc3ccc(Cl)c(Cl)c3)C(O)=O
• Formula: C20 H30 B Cl2 N2 O5
• Name: {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)
• ZINC: ZINC000263620640
• PDB chain: 4ixu Chain C Residue 406

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ixu Synthesis of quaternary alpha-amino acid-based arginase inhibitors via the Ugi reaction.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): H120 D143 H145 D147 S156 H160 D202 D251
• Binding residue (residue number reindexed from 1): H97 D120 H122 D124 S133 H137 D179 D228
• Annotation score: 1
• Binding affinity: MOAD: ic50=23nM

Enzymatic activity

• Catalytic site (original residue number in PDB): H120 D143 H145 D147 H160 D251 D253 E296
• Catalytic site (residue number reindexed from 1): H97 D120 H122 D124 H137 D228 D230 E273
• Enzyme Commision number: 3.5.3.1: arginase.

Gene Ontology

Molecular Function

• GO:0004053 arginase activity
• GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
• GO:0046872 metal ion binding

Biological Process

• GO:0006525 arginine metabolic process

External links

• PDB: RCSB:4ixu, PDBe:4ixu, PDBj:4ixu
• PDBsum: 4ixu
• PubMed: 23886684
• UniProt: P78540|ARGI2_HUMAN Arginase-2, mitochondrial (Gene Name=ARG2)