6RA7 | pdb_00006ra7

Human tnik in complex with compound 9

PDB DOI: https://doi.org/10.2210/pdb6RA7/pdb

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

Deposited: 2019-04-05 Released: 2019-11-06
Deposition Author(s): Read, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.189 (DCC)
R-Value Work:
0.174 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Tool inhibitors and assays to interrogate the biology of the TRAF2 and NCK interacting kinase

Read, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 35.49 kDa
Atom Count: 2,768
Modeled Residue Count: 302
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAF2 and NCK-interacting protein kinase	A	306	Homo sapiens	Mutation(s): 0 Gene Names: TNIK, KIAA0551 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKE5 (Homo sapiens) Explore Q9UKE5 Go to UniProtKB: Q9UKE5
PHAROS: Q9UKE5 GTEx: ENSG00000154310
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UKE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JWK (Subject of Investigation/LOI) Query on JWK 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]	2-[8-azanyl-2-(2-fluoranylpyridin-4-yl)-1,7-naphthyridin-5-yl]propan-2-ol C₁₆ H₁₅ F N₄ O XVUSMHCLFMFBQR-UHFFFAOYSA-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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
JWK	BindingDB: 6RA7	IC50: min: 126, max: 200 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.189 (DCC)
R-Value Work: 0.174 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.916	α = 90
b = 53.667	β = 90
c = 127.927	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XDS	data reduction
Aimless	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-11-06

Deposition Author(s):

Read, J.A.

Revision History (Full details and data files)

Version 1.0: 2019-11-06
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 6RA7 | pdb_00006ra7

Human tnik in complex with compound 9

Tool inhibitors and assays to interrogate the biology of the TRAF2 and NCK interacting kinase

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations