7K4I | pdb_00007k4i

Human Arginase 1 in complex with compound 06.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.253 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7K4I

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Comprehensive Strategies to Bicyclic Prolines: Applications in the Synthesis of Potent Arginase Inhibitors.

Li, D.Zhang, H.Lyons, T.W.Lu, M.Achab, A.Pu, Q.Childers, M.Mitcheltree, M.J.Wang, J.Martinot, T.A.McMinn, S.E.Sloman, D.L.Palani, A.Beard, A.Nogle, L.Gathiaka, S.Sauri, J.Kim, H.Y.Adpressa, D.Spacciapoli, P.Miller, J.R.Palte, R.L.Lesburg, C.A.Cumming, J.Fischer, C.

(2021) ACS Med Chem Lett 12: 1678-1688

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00258
  • Primary Citation Related Structures: 
    7K4G, 7K4H, 7K4I, 7K4J, 7K4K

  • PubMed Abstract: 

    Comprehensive synthetic strategies afforded a diverse set of structurally unique bicyclic proline-containing arginase inhibitors with a high degree of three-dimensionality. The analogs that favored the Cγ-exo conformation of the proline improved the arginase potency over the initial lead. The novel synthetic strategies reported here not only enable access to previously unknown stereochemically complex proline derivatives but also provide a foundation for the future synthesis of bicyclic proline analogs, which incorporate inherent three-dimensional character into building blocks, medicine, and catalysts and could have a profound impact on the conformation of proline-containing peptides and macrocycles.


  • Organizational Affiliation
    • Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.

Macromolecule Content 

  • Total Structure Weight: 210.91 kDa 
  • Atom Count: 15,380 
  • Modeled Residue Count: 1,902 
  • Deposited Residue Count: 1,932 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginase-1
A, B, C, D, E
A, B, C, D, E, F
322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
PHAROS:  P05089
GTEx:  ENSG00000118520 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VUY
(Subject of Investigation/LOI)

Query on VUY



Download:Ideal Coordinates CCD File
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
3-[(1~{S},2~{S},5~{R})-2-carboxy-6-thia-3-azabicyclo[3.2.0]heptan-1-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide
C9 H17 B N O5 S
UPRXFJNZWUYSLX-OOZYFLPDSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
J [auth B]
K [auth B]
M [auth C]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
S [auth E],
T [auth E],
V [auth F],
W [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.253 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.7α = 90
b = 287.1β = 90.28
c = 67.15γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-10-06 
  • Deposition Author(s): Palte, R.L.

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 2.0: 2021-12-08
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Refinement description