5AIK

Human DYRK1A in complex with LDN-211898

PDB DOI: https://doi.org/10.2210/pdb5AIK/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-15 Released: 2015-02-25
Deposition Author(s): Elkins, J.M., Soundararajan, M., Muniz, J.R.C., Cuny, G., Higgins, J., Edwards, A., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.252
R-Value Work: 0.227
R-Value Observed: 0.228

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Dyrk1A with Ldn-211898

Elkins, J.M., Soundararajan, M., Muniz, J.R.C., Cuny, G., Higgins, J., Edwards, A., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 180.51 kDa
Atom Count: 11,321
Modelled Residue Count: 1,374
Deposited Residue Count: 1,528
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A	A, B, C, D	382	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1 (PDB Primary Data), 2.7.12.1 (UniProt), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens) Explore Q13627 Go to UniProtKB: Q13627
PHAROS: Q13627 GTEx: ENSG00000157540
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13627
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AWR Query on AWR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	E [auth A], H [auth B], L [auth C], O [auth D]	4-(7-METHOXY-1-(TRIFLUOROMETHYL)-9H-PYRIDO[3,4-B]INDOL-9-yl)butan-1-amine C₁₇ H₁₈ F₃ N₃ O JVBWXORXTBDUMH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B, C, D	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.252
R-Value Work: 0.227
R-Value Observed: 0.228
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.955	α = 90
b = 90.891	β = 90
c = 232.468	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-25
Type: Initial release
Version 1.1: 2018-12-12
Changes: Data collection, Database references
Version 1.2: 2021-07-07
Changes: Derived calculations, Other, Refinement description
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary