GeezerVison is showing www.rcsb.org — RCSB PDB - 5IFO: X-ray structure of HSA-Myr-KP1019 5IFO | pdb_00005ifoX-ray structure of HSA-Myr-KP1019
Experimental Data Snapshot - Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free:
0.262 (Depositor), 0.273 (DCC) - R-Value Work:
0.244 (Depositor), 0.249 (DCC) - R-Value Observed:
0.245 (Depositor)
Starting Model: experimental View more details This is version 1.6 of the entry. See complete history. X-ray Structure Analysis of Indazolium trans-[Tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019) Bound to Human Serum Albumin Reveals Two Ruthenium Binding Sites and Provides Insights into the Drug Binding Mechanism.Bijelic, A., Theiner, S., Keppler, B.K., Rompel, A.(2016) J Med Chem 59: 5894-5903 - PubMed: 27196130 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1021/acs.jmedchem.6b00600
- Primary Citation Related Structures:
5IFO
- PubMed Abstract:
Ruthenium(III) complexes are promising candidates for anticancer drugs, especially the clinically studied indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019) and its analogue sodium trans-[tetrachlorobis(1H-indazole)ruthenate(III)] (NKP-1339). Several studies have emphasized the likely role of human serum proteins in the transportation and accumulation of ruthenium(III) complexes in tumors. Therefore, the interaction between KP1019 and human serum albumin was investigated by means of X-ray crystallography and inductively coupled plasma mass spectrometry (ICP-MS). The structural data unambiguously reveal the binding of two ruthenium atoms to histidine residues 146 and 242, which are both located within well-known hydrophobic binding pockets of albumin. The ruthenium centers are octahedrally coordinated by solvent molecules revealing the dissociation of both indazole ligands from the ruthenium-based drug. However, a binding mechanism is proposed indicating the importance of the indazole ligands for binding site recognition and thus their indispensable role for the binding of KP1019. Organizational Affiliation: - Fakultät für Chemie, Institut für Biophysikalische Chemie, Universität Wien , Althanstraße 14, 1090 Wien, Austria.
Macromolecule Content - Total Structure Weight: 68.14 kDa
- Atom Count: 4,682
- Modeled Residue Count: 582
- Deposited Residue Count: 585
- Unique protein chains: 1
Small Molecules| Ligands 2 Unique |
|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
|---|
MYR
Query on MYR
Download:Ideal Coordinates CCD File
- SDF format, chain I [auth A]
- SDF format, chain H [auth A]
- SDF format, chain G [auth A]
- SDF format, chain F [auth A]
- SDF format, chain E [auth A]
- SDF format, chain D [auth A]
- MOL2 format, chain I [auth A]
- MOL2 format, chain H [auth A]
- MOL2 format, chain G [auth A]
- MOL2 format, chain F [auth A]
- MOL2 format, chain E [auth A]
- MOL2 format, chain D [auth A]
- mmCIF format, chain I [auth A]
- mmCIF format, chain H [auth A]
- mmCIF format, chain G [auth A]
- mmCIF format, chain F [auth A]
- mmCIF format, chain E [auth A]
- mmCIF format, chain D [auth A]
| D [auth A] E [auth A] F [auth A] G [auth A] H [auth A]
D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A] | MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N |  | | RU
Query on RU
Download:Ideal Coordinates CCD File
| B [auth A], C [auth A] | RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N |  | |
Experimental Data & ValidationExperimental Data- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.262 (Depositor), 0.273 (DCC)
- R-Value Work: 0.244 (Depositor), 0.249 (DCC)
- R-Value Observed: 0.245 (Depositor)
Unit Cell: | Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 181.11 | α = 90 | | b = 38.06 | β = 105.06 | | c = 94.95 | γ = 90 |
Software Package:| Software Name | Purpose |
|---|
| PHENIX | refinement | | XDS | data scaling | | PHENIX | phasing | | XDS | data reduction |
Entry History & Funding InformationDeposition Data
| Funding Organization | Location | Grant Number |
|---|
| Austrian Science Fund | Austria | P23711 |
- Version 1.0: 2016-06-01
Type: Initial release
- Version 1.1: 2016-07-06
Changes: Database references - Version 1.2: 2017-09-06
Changes: Author supporting evidence - Version 1.3: 2018-01-31
Changes: Database references - Version 1.4: 2019-10-16
Changes: Data collection - Version 1.5: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.6: 2024-11-06
Changes: Structure summary
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