Download MendeleyStructure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor
Pachl, P., Simak, O., Rezacova, P., Fabry, M., Budesinsky, M., Rosenberg, I., Brynda, J.(2015) Medchemcomm 6: 1635-1638
4YIK
Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU
- PDB DOI: https://doi.org/10.2210/pdb4YIK/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-03-02 Released: 2015-09-09
- Funding Organization(s): Grant Agency of the Czech Republic
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.48 Å
- R-Value Free: 0.176
- R-Value Work: 0.153
- R-Value Observed: 0.154
Starting Model: experimental
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This is version 2.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 5'(3')-deoxyribonucleotidase, mitochondrial | 201 | Homo sapiens | Mutation(s): 0 Gene Names: NT5M, DNT2 EC: 3.1.3 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NPB1 (Homo sapiens) Explore Q9NPB1 Go to UniProtKB: Q9NPB1 | |||||
PHAROS: Q9NPB1 GTEx: ENSG00000205309 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NPB1 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 2O2 Query on 2O2 | G [auth A] | 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione C18 H20 N2 O11 P2 AYSYVLQGVXZPIY-OAIWFRFLSA-N |  | ||
| TRS Query on TRS | H [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| PEG Query on PEG | I [auth A], J [auth A], K [auth A], L [auth A], M [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | N [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| GOL Query on GOL | C [auth A], D [auth A], E [auth A], F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.48 Å
- R-Value Free: 0.176
- R-Value Work: 0.153
- R-Value Observed: 0.154
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 73.87 | α = 90 |
| b = 73.87 | β = 90 |
| c = 106.19 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PDB_EXTRACT | data extraction |
| SCALA | data scaling |
| REFMAC | refinement |
| MOSFLM | data reduction |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-09-09 Deposition Author(s): Pachl, P., Rezacova, P., Brynda, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Grant Agency of the Czech Republic | Czech Republic | -- |
Revision History (Full details and data files)
- Version 1.0: 2015-09-09
Type: Initial release - Version 2.0: 2017-09-06
Changes: Atomic model, Author supporting evidence, Derived calculations - Version 2.1: 2019-02-06
Changes: Data collection, Database references - Version 2.2: 2024-01-10
Changes: Data collection, Database references, Refinement description
