pentostatin

CHEBI:27834 ·resolve ·ANTIMICROBIAL_UNSPECIFIED ·EXACT REVIEWED

A member of the class of coformycins that is coformycin in which the hydroxy group at position 2' is replaced with a hydrogen. It is a drug used for the treatment of hairy cell leukaemia. — ChEBI

Classification

Strictly broader compounds or drug classes this molecule belongs to.

coformycins CHEBI:39304

Chemical structure

Computed structure properties
Molecular formula	C11H16N4O4
Charge	0
Average mass	268.273 Da
Monoisotopic mass	268.11716 Da
Source	ChEBI
InChIKey	FPVKHBSQESCIEP-JQCXWYLXSA-N

SMILES

OC[C@H]1O[C@@H](n2cnc3c2N=CNC[C@H]3O)C[C@@H]1O

InChI

InChI=1S/C11H16N4O4/c16-3-8-6(17)1-9(19-8)15-5-14-10-7(18)2-12-4-13-11(10)15/h4-9,16-18H,1-3H2,(H,12,13)/t6-,7+,8+,9+/m0/s1

Also called

Nipent (BRAND_NAME)— chebi
pentostatina (INN)— chebi
pentostatine (INN)— chebi
pentostatinum (INN)— chebi
(8R)-3-(2-deoxy-β-D-erythro-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol (EXACT_SYNONYM)— chebi
2'-deoxycoformycin (EXACT_SYNONYM)— chebi
CI 825 (EXACT_SYNONYM)— chebi
CI-825 (EXACT_SYNONYM)— chebi
CI825 (EXACT_SYNONYM)— chebi
PD 81565 (EXACT_SYNONYM)— chebi
PD-81565 (EXACT_SYNONYM)— chebi
PD-ADI (EXACT_SYNONYM)— chebi
PD81565 (EXACT_SYNONYM)— chebi
YK-176 (EXACT_SYNONYM)— chebi
co-vidarabine (EXACT_SYNONYM)— chebi
deoxycoformycin (EXACT_SYNONYM)— chebi

Cross-references

Identifiers for this same structure in other resources. An accession that lands on two different structures in this corpus is withheld from both rather than shown here, since it names at most one of them.

Drug registries

Identifiers that name a drug rather than a structure. One of these can cover a parent compound, its salts and its stereoisomers, which this corpus keeps as separate records, so it is not an equivalence of structure.

Patents and articles

Documents about this compound. A patent covers a class and an article covers a topic; neither identifies a structure.

Activity roles

Every antimicrobial role a source asserts for this compound — the unreduced evidence behind its antimicrobial_class.

nucleoside antibiotic CHEBI:25605

Source concepts

Every upstream concept that resolved to this record. The merge is the product: this is what shows ChEBI and CARD are describing the same structure.

Upstream concepts merged into this record
Source	Native ID	Label	Minted CURIE	Version
CHEBI	`CHEBI:27834`	pentostatin	`antibioticmech:chebi-04913c71fb`	2026-08-30

Molecular targets

The molecular entity or process this compound acts on. Each target carries evidence — this is a mechanistic claim, not a classification.

Adenosine deaminase PROTEIN MEASURED_TARGET_ASSOCIATION

BindingDB quantitative measurement in the named target organism; source assay descriptions and identifiers are retained per measurement. Evidence status: PRIMARY_EVIDENCE. Source: BINDINGDB 2026-09 (retrieved 2026-08-31).

Streptomyces antibioticus NCBITaxon:1890

Quantitative measurements
Type	Reported value	Assay	BindingDB IDs	Reference
KI	2.1 nM	In Vitro ADA Activity Assay For the ADA activity assay, a reaction comprising 50 mM potassium phosphate buffer (pH 7.2), 0.1 mM Ara-A or adenosine, and 20 mg ADA was conducted at 30 °C for 30 min. Reactions were terminated by the addition of an equivalent volume of methanol, followed by centrifugation to get rid of protein. The reactions were analyzed by HPLC (Shimadzu LC-20A), equipped with a reversephase C18 column (Inertsil ODS-3, 4.63250 mm, 5 mm), at the elution gradient of 5%-20% methanol:0.15% trifluoroacetic acid (TFA; HPLC grade) for 10 min, then the ratio of 20% methanol:0.15% TFA was continued until 30 min. The elution was monitored by a DAD at 260 nm with a flow rate of 0.5 mL/min. Assays were measured at ten different concentrations of substrate (adenosine, Ara-A) ranging from 10 to 100 mM in 50 mM potassium phosphate (pH 7.2) at 30 °C, and the assays were repeated at least three times. The inhibitory activity of PTN was assayed by adding differentconcentrations (final concentrations 1, 2, and 5 nM) to the reaction mixture described above.	`RSID 390254` `assay 7900_1` `monomer 223291`	`PMID:28111097`
KI	1 nM	In Vitro ADA Activity Assay For the ADA activity assay, a reaction comprising 50 mM potassium phosphate buffer (pH 7.2), 0.1 mM Ara-A or adenosine, and 20 mg ADA was conducted at 30 °C for 30 min. Reactions were terminated by the addition of an equivalent volume of methanol, followed by centrifugation to get rid of protein. The reactions were analyzed by HPLC (Shimadzu LC-20A), equipped with a reversephase C18 column (Inertsil ODS-3, 4.63250 mm, 5 mm), at the elution gradient of 5%-20% methanol:0.15% trifluoroacetic acid (TFA; HPLC grade) for 10 min, then the ratio of 20% methanol:0.15% TFA was continued until 30 min. The elution was monitored by a DAD at 260 nm with a flow rate of 0.5 mL/min. Assays were measured at ten different concentrations of substrate (adenosine, Ara-A) ranging from 10 to 100 mM in 50 mM potassium phosphate (pH 7.2) at 30 °C, and the assays were repeated at least three times. The inhibitory activity of PTN was assayed by adding differentconcentrations (final concentrations 1, 2, and 5 nM) to the reaction mixture described above.	`RSID 390255` `assay 7900_1` `monomer 223291`	`PMID:28111097`

Organism-specific examples
Protein	Gene	Organism	Entry
Adenosine deaminase `UniProtKB:A0A1S5RQP7` BindingDB target chain 1	—	Streptomyces antibioticus `NCBITaxon:1890`	UNREVIEWED

PMID:28111097 (BindingDB literature-curated quantitative target measurement; source value, assay text, reaction-set ID, and target organism retained.)

adenosine deaminase PROTEIN DIRECT_BINDING_TARGET

A P. vivax ADA cocrystal with the picomolar inhibitor 2'-deoxycoformycin defined inhibitor recognition and a parasite-specific substrate-induced conformational change. Evidence status: PRIMARY_EVIDENCE. Source: PRIMARY_LITERATURE 2008-06 (retrieved 2026-09-02).

PMID:18602399 (Primary pentostatin-bound Plasmodium vivax ADA structure (DOI:10.1016/j.jmb.2008.06.048).)

Mechanism summary

Mode of action: OTHER host shared target — CURATOR: PMID:18602399 resolved pentostatin (2'-deoxycoformycin) bound to Plasmodium vivax adenosine deaminase, a central enzyme in parasite purine salvage. The conserved enzyme is host-shared, while the structures identify parasite-specific conformational and substrate-recognition features that may support selectivity.
Clinical status: APPROVED

Record-level evidence

PMID:18602399 (Primary exact-pentostatin P. vivax adenosine-deaminase cocrystal and selectivity study.)

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (CHEBI)
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories
REVIEWED 2026-09-02 · codex · LLM-assisted
Verified exact ChEBI identity, structure, role, unspecified filing class, retained BindingDB measurements, and retained FDA assertions; added purine-salvage inhibition and the directly bound P. vivax ADA target.
RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources
Re-seeded from updated data/raw/ inventories

Provenance

Seeded by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record (YAML).

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