7ACH | pdb_00007ach

CRYSTAL STRUCTURE OF ACTIVE KRAS G12D (GPPCP) IN COMPLEX WITH THE SOAKED DIMERIC INHIBITOR BI-5747

PDB DOI: https://doi.org/10.2210/pdb7ACH/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-09-10 Released: 2020-11-18
Deposition Author(s): Kessler, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.214 (Depositor), 0.225 (DCC)
R-Value Work:
0.173 (Depositor), 0.177 (DCC)
R-Value Observed:
0.175 (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

CRYSTAL STRUCTURE OF ACTIVE KRAS G12D (GPPCP) IN COMPLEX WITH THE SOAKED DIMERIC INHIBITOR BI-5747

Kessler, D.

To be published.

Macromolecule Content

Total Structure Weight: 40.53 kDa
Atom Count: 2,972
Modeled Residue Count: 334
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, B	170	Homo sapiens	Mutation(s): 1 Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116 Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R6W (Subject of Investigation/LOI) Query on R6W Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3~{S})-5-oxidanyl-3-[2-[[6-[[3-[(1~{S})-6-oxidanyl-3-oxidanylidene-1,2-dihydroisoindol-1-yl]-1~{H}-indol-2-yl]methylamino]hexylamino]methyl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one C₄₀ H₄₀ N₆ O₄ LWNXLGGZVHNJBW-UWXQCODUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GCP Query on GCP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.214 (Depositor), 0.225 (DCC)
R-Value Work: 0.173 (Depositor), 0.177 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.018	α = 90
b = 72.773	β = 103.57
c = 54.437	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Kessler, D.

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2024-01-31
Changes: Advisory, Data collection, Database references, Refinement description