3CY3

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and the JNK inhibitor V

PDB DOI: https://doi.org/10.2210/pdb3CY3/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-04-25 Released: 2008-07-15
Deposition Author(s): Filippakopoulos, P., Bullock, A., Fedorov, O., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.205
R-Value Work: 0.163
R-Value Observed: 0.165

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and the JNK inhibitor V.

Filippakopoulos, P., Bullock, A., Fedorov, O., Pike, A.C.W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 37.83 kDa
Atom Count: 2,509
Modelled Residue Count: 279
Deposited Residue Count: 328
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	314	Homo sapiens	Mutation(s): 1 Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309 Go to UniProtKB: P11309
PHAROS: P11309 GTEx: ENSG00000137193
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11309
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pimtide peptide	B	14	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JN5 Query on JN5 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(2S)-1,3-benzothiazol-2-yl{2-[(2-pyridin-3-ylethyl)amino]pyrimidin-4-yl}ethanenitrile C₂₀ H₁₆ N₆ S RCYPVQCPYKNSTG-OAHLLOKOSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
JN5	BindingDB: 3CY3	IC50: 80 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.205
R-Value Work: 0.163
R-Value Observed: 0.165
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.239	α = 90
b = 98.239	β = 90
c = 80.723	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-15

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-07-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2022-02-16
Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description
Version 1.6: 2024-10-30
Changes: Structure summary