7ULU

Human DDAH1 soaked with its inhibitor ClPyrAA

PDB DOI: https://doi.org/10.2210/pdb7ULU/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-05 Released: 2023-08-30
Deposition Author(s): Butrin, A., Zheng, Y., Tuley, A., Liu, D., Fast, W.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267
R-Value Work: 0.207
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Optimization of a switchable electrophile fragment into a potent and selective covalent inhibitor of human DDAH1

Tuley, A., Zheng, Y., Tommasi, S., Butrin, A., May, K.V., Ahn, Y., Reidl, T.C., Weerakoon, L., Hulin, J., Meech, R., Patel, D.S., Horton, C.P., Swartzel, C.J., Kim, Y., Silverman, B.R., Mangoni, A., Liu, D., Fast, W.

To be published.

Macromolecule Content

Total Structure Weight: 67.64 kDa
Atom Count: 4,268
Modelled Residue Count: 550
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1	A, B	308	Homo sapiens	Mutation(s): 0 Gene Names: DDAH1, DDAH EC: 3.5.3.18
UniProt & NIH Common Fund Data Resources
Find proteins for O94760 (Homo sapiens) Explore O94760 Go to UniProtKB: O94760
PHAROS: O94760 GTEx: ENSG00000153904
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O94760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NOU (Subject of Investigation/LOI) Query on NOU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	(2S)-2-amino-4-[(pyridin-2-yl)amino]butanoic acid C₉ H₁₃ N₃ O₂ QJIQHEBKRNDRHG-ZETCQYMHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267
R-Value Work: 0.207
R-Value Observed: 0.210
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.81	α = 90
b = 46.85	β = 109.15
c = 80.27	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1904514

Revision History (Full details and data files)

Version 1.0: 2023-08-30
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.