9HN6 | pdb_00009hn6

X-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with ribonuclease A

  • Classification: HYDROLASE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2024-12-10 Released: 2025-05-14 
  • Deposition Author(s): Ferraro, G., Merlino, A.
  • Funding Organization(s): NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.215 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9HN6

This is version 1.1 of the entry. See complete history

Literature

Cytotoxicity and Binding to DNA, Lysozyme, Ribonuclease A, and Human Serum Albumin of the Diiodido Analog of Picoplatin.

Ferraro, G.Pracharova, J.Gotte, G.Massai, L.Berecka, M.Starha, P.Messori, L.Merlino, A.

(2025) Inorg Chem 64: 8895-8905

  • DOI: https://doi.org/10.1021/acs.inorgchem.4c05424
  • Primary Citation Related Structures: 
    9HLK, 9HMK, 9HMQ, 9HN6, 9HNB

  • PubMed Abstract: 

    Here we investigated cytotoxicity and DNA and protein binding of an iodido analog of picoplatin, the cis -ammine-diiodido(2-methylpyridine)platinum(II) complex (I-picoplatin). I-picoplatin (IC 50 = 3.7-12.4 μM) outperforms picoplatin (IC 50 = 11.8-22.6 μM) in the human cancer cell lines used and shows a greater ability to overcome the cisplatin resistance of A2780 ovarian cancer cells than does picoplatin. I-picoplatin also induces different cell cycle changes (reduced S-phase fraction and an increase in the G2/M phase arrest) in HeLa cervical carcinoma cells compared to both picoplatin and cisplatin. Binding of the metal compound to DNA model systems was investigated by ethidium bromide displacement assay and circular dichroism. Its reactivity with lysozyme (HEWL) and pancreatic RNase A was studied by X-ray diffraction and mass spectrometry experiments. I-picoplatin binds the DNA double helix and is able to retain the 2-methylpyridine ligand and at least one of the two iodido ligands when bound to the two proteins. Various Pt-containing moieties, including one based on the isomerized structure of I-picoplatin, coordinate the His and Met residues. A low-resolution structure of the I-picoplatin/human serum albumin (HSA) adduct has also been solved. The side chains of His146, Met289, and Met329 are the primary binding sites of the I-picoplatin moieties on HSA.


  • Organizational Affiliation
    • Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cinthia 21, Naples 80126, Italy.

Macromolecule Content 

  • Total Structure Weight: 31.36 kDa 
  • Atom Count: 2,053 
  • Modeled Residue Count: 241 
  • Deposited Residue Count: 248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonuclease pancreaticA [auth AAA],
B [auth BBB]
124Bos taurusMutation(s): 0 
EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT
(Subject of Investigation/LOI)

Query on PT



Download:Ideal Coordinates CCD File
AA [auth BBB]
F [auth AAA]
G [auth AAA]
H [auth AAA]
I [auth AAA]
AA [auth BBB],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
U [auth BBB],
V [auth BBB],
W [auth BBB],
X [auth BBB],
Y [auth BBB],
Z [auth BBB]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
BA [auth BBB]
CA [auth BBB]
DA [auth BBB]
EA [auth BBB]
FA [auth BBB]
BA [auth BBB],
CA [auth BBB],
DA [auth BBB],
EA [auth BBB],
FA [auth BBB],
M [auth AAA],
N [auth AAA],
O [auth AAA],
P [auth AAA],
Q [auth AAA]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
R [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NH3

Query on NH3



Download:Ideal Coordinates CCD File
C [auth AAA]
D [auth AAA]
E [auth AAA]
L [auth AAA]
S [auth BBB]
C [auth AAA],
D [auth AAA],
E [auth AAA],
L [auth AAA],
S [auth BBB],
T [auth BBB]
AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.215 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.04α = 90
b = 32.64β = 90.109
c = 73.45γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)Italy2022JMFC3X

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references