BMRB Entry 30694

Name: The HADDOCK structure model of GDP KRas in complex with its allosteric inhibitor E22
Published: 2019-12-10

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PDB ID: 6v5l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30694
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: The HADDOCK structure model of GDP KRas in complex with its allosteric inhibitor E22 PubMed: 30903639

Deposition date: 2019-12-04 Original release date: 2019-12-10

Authors: Wang, X.; Gupta, A.; Prakash, P.; Putkey, J.; Gorfe, A.

Citation: Gupta, A.; Wang, X.; Pagba, C.; Prakash, P.; Putkey, J.; Gorfe, A.. "Multi target ensemble based virtual screening yields novel allosteric KRAS inhibitors at high success rate" Chem. Biol. Drug Des. 94, 1441-1456 (2019).

Assembly members:
entity_1, polymer, 169 residues, 19271.760 Da.
entity_GDP, non-polymer, 443.201 Da.
entity_MG, non-polymer, 24.305 Da.
entity_QPD, non-polymer, 308.335 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: MTEYKLVVVGAGGVGKSALT IQLIQNHFVDEYDPTIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHHYREQI KRVKDSEDVPMVLVGNKCDL PSRTVDTKQAQDLARSYGIP FIETSAKTRQGVDDAFYTLV REIRKHKEK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	160
1H chemical shifts	160

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_3	3
4	entity_4	4

Entities:

Entity 1, entity_1 169 residues - 19271.760 Da.

1

MET

THR

GLU

TYR

LYS

LEU

VAL

GLY

2

ALA

GLY

VAL

GLY

LYS

SER

ALA

LEU

THR

3

ILE

GLN

LEU

ILE

GLN

ASN

HIS

PHE

VAL

ASP

4

GLU

TYR

ASP

PRO

THR

ILE

GLU

ASP

SER

TYR

5

ARG

LYS

GLN

VAL

ILE

ASP

GLY

GLU

THR

6

CYS

LEU

ASP

ILE

LEU

ASP

THR

ALA

GLY

7

GLN

GLU

TYR

SER

ALA

MET

ARG

ASP

GLN

8

TYR

MET

ARG

THR

GLY

GLU

GLY

PHE

LEU

CYS

9

VAL

PHE

ALA

ILE

ASN

THR

LYS

SER

PHE

10

GLU

ASP

ILE

HIS

TYR

ARG

GLU

GLN

ILE

11

LYS

ARG

VAL

LYS

ASP

SER

GLU

ASP

VAL

PRO

12

MET

VAL

LEU

VAL

GLY

ASN

LYS

CYS

ASP

LEU

13

PRO

SER

ARG

THR

VAL

ASP

THR

LYS

GLN

ALA

14

GLN

ASP

LEU

ALA

ARG

SER

TYR

GLY

ILE

PRO

15

PHE

ILE

GLU

THR

SER

ALA

LYS

THR

ARG

GLN

16

GLY

VAL

ASP

ALA

PHE

TYR

THR

LEU

VAL

17

ARG

GLU

ILE

ARG

LYS

HIS

LYS

GLU

LYS

Entity 2, entity_2 - C10 H15 N5 O11 P2 - 443.201 Da.

1

GDP

Entity 3, entity_3 - Mg - 24.305 Da.

1

MG

Entity 4, entity_4 - C17 H16 N4 O2 - 308.335 Da.

1

QPD

Samples:

sample_1: KRAS, [U-99% 13C; U-99% 15N], 0.8 mM; E22 1.0 mM; DTT, [U-99% 2H], 5 mM; DSS, [U-99% 2H], 10 uM; sodium phosphate, nature abundance, 25 mM; sodium chloride 50 mM; MAGNESIUM ION 5 mM

sample_2: E22 1.0 mM; DTT, [U-99% 2H], 5 mM; DSS, [U-99% 2H], 10 uM; sodium phosphate 25 mM; sodium chloride 50 mM; MAGNESIUM ION 5 mM; KRas, [U-99% 13C; U-99% 15N], 0.8 mM

sample_conditions_1: ionic strength: 115 mM; pH: 7.4; pressure: 1 Pa; temperature: 298 K

sample_conditions_2: ionic strength: 115 mM; pH: 7.4 pD; pressure: 1 Pa; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D NOESY 15N HSQC	sample_1	isotropic	sample_conditions_1
2D 15N HSQC	sample_1	isotropic	sample_conditions_1
2D 13C HSQC	sample_2	isotropic	sample_conditions_2
3D CCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D NOESY 13C HSQC	sample_2	isotropic	sample_conditions_2
F1 13C 15N filtered 3D NOESY 13C HSQC	sample_2	isotropic	sample_conditions_2

Software:

TopSpin v2, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

HADDOCK, Bonvin - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts