4ZOG | pdb_00004zog

VX-680/MK-0457 binds to human ABL1 also in inactive DFG conformations.

PDB DOI: https://doi.org/10.2210/pdb4ZOG/pdb

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

Deposited: 2015-05-06 Released: 2016-09-14
Deposition Author(s): Kyomuhendo, P., Narayanan, D., Engh, R.A.
Funding Organization(s): Tromso Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

VX-680/MK-0457 binds also to human ABL1 with inactive DFG conformations.

Kyomuhendo, P., Narayanan, D., Engh, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 66.89 kDa
Atom Count: 4,479
Modelled Residue Count: 537
Deposited Residue Count: 566
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 kinase ABL1	A, B	283	Homo sapiens	Mutation(s): 0 Gene Names: ABL1, ABL, JTK7 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens) Explore P00519 Go to UniProtKB: P00519
PHAROS: P00519 GTEx: ENSG00000097007
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00519
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VX6 Query on VX6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE C₂₃ H₂₈ N₈ O S GCIKSSRWRFVXBI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MXE Query on MXE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	2-METHOXYETHANOL C₃ H₈ O₂ XNWFRZJHXBZDAG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
VX6	BindingDB: 4ZOG	Ki: min: 30, max: 42 (nM) from 2 assay(s)
		Kd: min: 3, max: 1.70e+4 (nM) from 31 assay(s)
		IC50: min: 50, max: 420 (nM) from 5 assay(s)