5KMA

Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N mutant nucleoside D-Trp phosphoramidate substrate complex

Summary for 5KMA

• Entry DOI: 10.2210/pdb5kma/pdb
• Related: 3TW2 5IPB 5IPC 5IPD 5IPE 5KLY 5KLZ 5KM0 5KM1 5KM2 5KM3 5KM4 5KM5 5KM6 5KM7 5KM8 5KM9 5KMB 5KMC
• Descriptor: Histidine triad nucleotide-binding protein 1, [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-ethyl-phosphonamidic acid, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: hint, histidine triad, hit, hydrolase
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm: P49773
• Total number of polymer chains: 2
• Total formula weight: 28570.03

Authors

Maize, K.M.,Finzel, B.C. (deposition date: 2016-06-26, release date: 2017-06-28, Last modification date: 2023-09-27)

Primary citation

Maize, K.M.,Shah, R.,Strom, A.,Kumarapperuma, S.,Zhou, A.,Wagner, C.R.,Finzel, B.C.
A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides.
Mol. Pharm., 14:3987-3997, 2017

PubMed Abstract: Nucleotide analogues that incorporate a metabolically labile nucleoside phosphoramidate (a ProTide) have found utility as prodrugs. In humans, ProTides can be cleaved by human histidine triad nucleotide binding protein 1 (hHint1) to expose the nucleotide monophosphate. Activation by this route circumvents highly selective nucleoside kinases that limit the use of nucleosides as prodrugs. To better understand the diversity of potential substrates of hHint1, we created and studied a series of phosphoramidate nucleosides. Using a combination of enzyme kinetics, X-ray crystallography, and isothermal titration calorimetry with both wild-type and inactive mutant enzymes, we have been able to explore the energetics of substrate binding and establish a structural basis for catalytic efficiency. Diverse nucleobases are well tolerated, but portions of the ribose are needed to position substrates for catalysis. Beneficial characteristics of the amine leaving group are also revealed. Structural principles revealed by these results may be exploited to tune the rate of substrate hydrolysis to strategically alter the intracellular release of the product nucleoside monophosphate from the ProTide.

PubMed: 28968488
DOI: 10.1021/acs.molpharmaceut.7b00664

Experimental method

X-RAY DIFFRACTION (1.55 Å)