6BRC | pdb_00006brc

Crystal Structure of the Human CAMKK2B in complex with AP26113-analog (ALK-IN-1)

PDB DOI: https://doi.org/10.2210/pdb6BRC/pdb

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

Deposited: 2017-11-30 Released: 2017-12-13
Deposition Author(s): Counago, R.M., dos Reis, C.V., de Souza, G.P., Ramos, P.Z., Drewry, D., Massirer, K.B., Arruda, P., Edwards, A.M., Elkins, J.M., Structural Genomics Consortium (SGC)
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.265 (Depositor), 0.268 (DCC)
R-Value Work:
0.213 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Human CAMKK2B in complex with AP26113-analog (ALK-IN-1)

Counago, R.M., dos Reis, C.V., de Souza, G.P., Ramos, P.Z., Drewry, D., Massirer, K.B., Arruda, P., Edwards, A.M., Elkins, J.M., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 67.34 kDa
Atom Count: 4,120
Modeled Residue Count: 525
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase kinase 2	A, B	291	Homo sapiens	Mutation(s): 0 Gene Names: CAMKK2, CAMKKB, KIAA0787 EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RR4 (Homo sapiens) Explore Q96RR4 Go to UniProtKB: Q96RR4
PHAROS: Q96RR4 GTEx: ENSG00000110931
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96RR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E5J Query on E5J Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	5-chloro-N~2~-{4-[4-(dimethylamino)piperidin-1-yl]-2-methoxyphenyl}-N~4~-[2-(dimethylphosphoryl)phenyl]pyrimidine-2,4-diamine C₂₆ H₃₄ Cl N₆ O₂ P OVDSPTSBIQCAIN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.265 (Depositor), 0.268 (DCC)
R-Value Work: 0.213 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.8	α = 72.38
b = 54.861	β = 78.35
c = 56.633	γ = 89.74

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5

Revision History (Full details and data files)

Version 1.0: 2017-12-13
Type: Initial release
Version 1.1: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description