6BRC

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), 0.270 (DCC)
R-Value Work:
0.213 (Depositor), 0.220 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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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
Modelled Residue Count: 525
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96RR4
Sequence Annotations Expand
Reference Sequence LOADING

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 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]	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), 0.270 (DCC)
R-Value Work: 0.213 (Depositor), 0.220 (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

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