2CMC

Structural Basis for Inhibition of Protein Tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics

PDB DOI: https://doi.org/10.2210/pdb2CMC/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-05-04 Released: 2006-08-17
Deposition Author(s): Ala, P.J., Gonneville, L., Hillman, M.C., Becker-Pasha, M., Wei, M., Reid, B.G., Klabe, R., Yue, E.W., Wayland, B., Douty, B., Combs, A.P., Polam, P., Wasserman, Z., Bower, M., Burn, T.C., Hollis, G.F., Wynn, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.263
R-Value Work: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 36.42 kDa
Atom Count: 2,577
Modelled Residue Count: 286
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1	A	304	Homo sapiens	Mutation(s): 0 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031 Go to UniProtKB: P18031
PHAROS: P18031 GTEx: ENSG00000196396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DFM Query on DFM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-ACETYL-L-PHENYLALANYL-4-[DIFLUORO(PHOSPHONO)METHYL]-L-PHENYLALANINAMIDE C₂₁ H₂₄ F₂ N₃ O₆ P KPMMESISHWWXNM-ROUUACIJSA-N		Interactions Focus chain B [auth A]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
DFM	BindingDB: 2CMC	IC50: min: 1700, max: 1.75e+6 (nM) from 3 assay(s)
	PDBBind: 2CMC	IC50: 1750 (nM) from 1 assay(s)
	Binding MOAD: 2CMC	IC50: 1750 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.263
R-Value Work: 0.209
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.2	α = 90
b = 70.9	β = 90
c = 83.31	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-17
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-07-05
Changes: Data collection
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

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Help and Resources

2CMC

Structural Basis for Inhibition of Protein Tyrosine Phosphatase 1B by Isothiazolidinone Heterocyclic Phosphonate Mimetics

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)