7Z5N | pdb_00007z5n

Crystal structure of DYRK1A in complex with CX-4945

PDB DOI: https://doi.org/10.2210/pdb7Z5N/pdb

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

Deposited: 2022-03-09 Released: 2023-03-22
Deposition Author(s): Pustelny, K., Grygier, P., Golik, P., Dubin, G., Czarna, A.
Funding Organization(s): Polish National Science Centre, National Center for Research and Development (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.252 (Depositor), 0.252 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure DYRK1A in complex with CX-4945

Grygier, P., Pustelny, K., Golik, P., Popowicz, G., Dubin, G., Czarna, A.

To be published.

Macromolecule Content

Total Structure Weight: 353.44 kDa
Atom Count: 21,926
Modeled Residue Count: 2,697
Deposited Residue Count: 2,960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B, C, D, E A, B, C, D, E, F, G, H	370	Homo sapiens	Mutation(s): 0 Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.12.1 (PDB Primary Data), 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13627
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3NG Query on 3NG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth F] SDF format, chain U [auth B] SDF format, chain TA [auth E] SDF format, chain OA [auth D] SDF format, chain JB [auth H] SDF format, chain I [auth A] SDF format, chain GA [auth C] SDF format, chain CB [auth G] MOL2 format, chain ZA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain OA [auth D] MOL2 format, chain JB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain CB [auth G] mmCIF format, chain ZA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain OA [auth D] mmCIF format, chain JB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain CB [auth G]	CB [auth G] GA [auth C] I [auth A] JB [auth H] OA [auth D] CB [auth G], GA [auth C], I [auth A], JB [auth H], OA [auth D], TA [auth E], U [auth B], ZA [auth F]	5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid C₁₉ H₁₂ Cl N₃ O₂ MUOKSQABCJCOPU-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain GA [auth C] Focus chain I [auth A] Focus chain JB [auth H] Focus chain OA [auth D] Focus chain TA [auth E] Focus chain U [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain CB [auth G] Focus chain GA [auth C] Focus chain I [auth A] Focus chain JB [auth H] Focus chain OA [auth D] Focus chain TA [auth E] Focus chain U [auth B] Focus chain ZA [auth F]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain WA [auth E] SDF format, chain SA [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain LB [auth H] SDF format, chain KA [auth C] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain SA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain LB [auth H] MOL2 format, chain KA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain SA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain LB [auth H] mmCIF format, chain KA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] KA [auth C] LB [auth H] O [auth A] AA [auth B], BA [auth B], KA [auth C], LB [auth H], O [auth A], P [auth A], SA [auth D], WA [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LB [auth H] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth D] Focus chain WA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain LB [auth H] Focus chain O [auth A] Focus chain P [auth A] Focus chain SA [auth D] Focus chain WA [auth E]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain MB [auth H] SDF format, chain FA [auth B] MOL2 format, chain MB [auth H] MOL2 format, chain FA [auth B] mmCIF format, chain MB [auth H] mmCIF format, chain FA [auth B]	FA [auth B], MB [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain MB [auth H] Interactions & Density Focus chain FA [auth B] Focus chain MB [auth H]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain XA [auth E] SDF format, chain Q [auth A] SDF format, chain GB [auth G] SDF format, chain FB [auth G] MOL2 format, chain XA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain GB [auth G] MOL2 format, chain FB [auth G] mmCIF format, chain XA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain GB [auth G] mmCIF format, chain FB [auth G]	FB [auth G], GB [auth G], Q [auth A], XA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FB [auth G] Focus chain GB [auth G] Focus chain Q [auth A] Focus chain XA [auth E] Interactions & Density Focus chain FB [auth G] Focus chain GB [auth G] Focus chain Q [auth A] Focus chain XA [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain VA [auth E] SDF format, chain V [auth B] SDF format, chain UA [auth E] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain PA [auth D] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KB [auth H] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain EB [auth G] SDF format, chain DB [auth G] SDF format, chain AB [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth H] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain AB [auth F] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth H] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain AB [auth F]	AB [auth F] DB [auth G] EB [auth G] HA [auth C] IA [auth C] AB [auth F], DB [auth G], EB [auth G], HA [auth C], IA [auth C], J [auth A], JA [auth C], K [auth A], KB [auth H], L [auth A], M [auth A], N [auth A], PA [auth D], QA [auth D], RA [auth D], UA [auth E], V [auth B], VA [auth E], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KB [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KB [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain YA [auth E] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain IB [auth G] SDF format, chain HB [auth G] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BB [auth F] MOL2 format, chain YA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain IB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth F] mmCIF format, chain YA [auth E] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain IB [auth G] mmCIF format, chain HB [auth G] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth F]	BB [auth F] CA [auth B] DA [auth B] EA [auth B] HB [auth G] BB [auth F], CA [auth B], DA [auth B], EA [auth B], HB [auth G], IB [auth G], LA [auth C], MA [auth C], NA [auth C], R [auth A], S [auth A], T [auth A], YA [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain YA [auth E] Interactions & Density Focus chain BB [auth F] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain YA [auth E]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
3NG	BindingDB: 7Z5N	Kd: min: 0.77, max: 35 (nM) from 3 assay(s)
3NG	BindingDB: 7Z5N	IC50: min: 1.9, max: 160 (nM) from 5 assay(s)