Macromolecule Content

Total Structure Weight: 136142.56
Atom Count: 8613
Residue Count: 1158
Unique protein chains: 2

4AZE

Human DYRK1A in complex with Leucettine L41

DOI: 10.2210/pdb4AZE/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)

Deposited: 2012-06-25 Released: 2012-09-05
Deposition Author(s): Elkins, J.M., Soundararajan, M., Muniz, J.R.C., Tahtouh, T., Burgy, G., Durieu, E., Lozach, O., Cochet, C., Schmid, R.S., Lo, D.C., Delhommel, F., Carreaux, F., Bazureau, J.P., Meijer, L., Edwards, A., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.248
R-Value Work: 0.218

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Selectivity, Co-Crystal Structures and Neuroprotective Properties of Leucettines, a Family of Protein Kinase Inhibitors Derived from the Marine Sponge Alkaloid Leucettamine B.

Tahtouh, T., Elkins, J.M., Filippakopoulos, P., Soundararajan, M., Burgy, G., Durieu, E., Cochet, C., Schmid, R.S., Lo, D.C., Delhommel, F., Oberholzer, A., Laurence, P., Carreaux, F., Bazureau, J.P., Knapp, S., Meijer, L.

(2012) J.Med.Chem. 55: 9312

PubMed: 22998443 Search on PubMed
DOI: 10.1021/jm301034u
Primary Citation of Related Structures:
4GW8, 4B7T, 4AZF

PubMed Abstract:

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A	A, B, C	382	Homo sapiens	Mutation(s): 0 Gene Names: DYRK1A (DYRK, MNB, MNBH) EC: 2.7.12.1
Find proteins for Q13627 (Homo sapiens) Go to Gene View: DYRK1A Go to UniProtKB: Q13627
Protein Feature View Full Protein Feature View for Q13627

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A	E, F, G	4	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
3RA Query on 3RA Download SDF File Download CCD File	A, B, C	5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one C₁₇ H₁₃ N₃ O₃ ZDINVWCJHPMIKS-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, C, E, F, G	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
UNK Query on UNK	E, F, G	L-PEPTIDE LINKING	C₄ H₉ N O₂		--
PTR Query on PTR	A, B, C	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
3RA	Kd: 7.8 nM PDBBIND

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.248
R-Value Work: 0.218
Space Group: P 3₁ 1 2

Unit Cell:

Length (Å)	Angle (°)
a = 111.649	α = 90.00
b = 111.649	β = 90.00
c = 301.725	γ = 120.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2012-06-25
Released Date: 2012-09-05
Deposition Author(s): Elkins, J.M., Soundararajan, M., Muniz, J.R.C., Tahtouh, T., Burgy, G., Durieu, E., Lozach, O., Cochet, C., Schmid, R.S., Lo, D.C., Delhommel, F., Carreaux, F., Bazureau, J.P., Meijer, L., Edwards, A., Bountra, C., Knapp, S.

Revision History

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2012-10-03
Type: Database references, Derived calculations
Version 1.2: 2012-11-21
Type: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the National Institutes of Health, and the US Department of Energy (DE-SC0019749).