6T6F | pdb_00006t6f

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 8 (CS275)

PDB DOI: https://doi.org/10.2210/pdb6T6F/pdb

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

Deposited: 2019-10-18 Released: 2020-01-15
Deposition Author(s): Sorrell, F., Kraemer, A., Butterworth, S., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

CAMK1D bound to CS275

Sorrell, F., Kraemer, A., Butterworth, S., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 74.16 kDa
Atom Count: 4,753
Modeled Residue Count: 575
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase type 1D	A, B	322	Homo sapiens	Mutation(s): 0 Gene Names: CAMK1D, CAMKID EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU85 (Homo sapiens) Explore Q8IU85 Go to UniProtKB: Q8IU85
PHAROS: Q8IU85 GTEx: ENSG00000183049
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IU85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MMW (Subject of Investigation/LOI) Query on MMW Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3-(trifluoromethyl)phenyl]amino]pyrimidine-5-carboxamide C₁₇ H₁₉ F₃ N₆ O ASMLDRAEBPYENO-NSHDSACASA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
MMW	BindingDB: 6T6F	IC50: min: 179, max: 186 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.238 (Depositor), 0.239 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.95	α = 90
b = 115.73	β = 90
c = 53.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
xia2	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Butterworth, S.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202708

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.