Download MendeleyStructure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835
Anand, K., Schmitz, M., Geyer, M.To be published.
9FMR
Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835
- PDB DOI: https://doi.org/10.2210/pdb9FMR/pdb
- Classification: TRANSCRIPTION
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2024-06-07 Released: 2024-10-16
- Funding Organization(s): German Research Foundation (DFG)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.90 Å
- R-Value Free: 0.250
- R-Value Work: 0.208
- R-Value Observed: 0.209
Starting Models: experimental
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This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA damage-binding protein 1 | 864 | Homo sapiens | Mutation(s): 0 Gene Names: DDB1, XAP1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531 | |||||
PHAROS: Q16531 GTEx: ENSG00000167986 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q16531 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cyclin-dependent kinase 12 | 351 | Homo sapiens | Mutation(s): 0 Gene Names: CDK12, CRK7, CRKRS, KIAA0904 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NYV4 (Homo sapiens) Explore Q9NYV4 Go to UniProtKB: Q9NYV4 | |||||
PHAROS: Q9NYV4 GTEx: ENSG00000167258 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NYV4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cyclin-K | 268 | Homo sapiens | Mutation(s): 0 Gene Names: CCNK, CPR4 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75909 (Homo sapiens) Explore O75909 Go to UniProtKB: O75909 | |||||
PHAROS: O75909 GTEx: ENSG00000090061 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O75909 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| RMF (Subject of Investigation/LOI) Query on RMF | J [auth B], K [auth E], L [auth H] | ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine C21 H20 Cl2 N10 O FSELUFUYNUNZKD-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TPO Query on TPO | B, E, H | L-PEPTIDE LINKING | C4 H10 N O6 P |  | THR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.90 Å
- R-Value Free: 0.250
- R-Value Work: 0.208
- R-Value Observed: 0.209
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 249.521 | α = 90 |
| b = 249.521 | β = 90 |
| c = 218.535 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-10-16 Deposition Author(s): Anand, K., Schmitz, M., Geyer, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| German Research Foundation (DFG) | Germany | EXC2151-390873048 |
Revision History (Full details and data files)
- Version 1.0: 2024-10-16
Type: Initial release
