Structure

Physi-Chem Properties

Molecular Weight:  260.03
Volume:  242.021
LogP:  1.878
LogD:  1.937
LogS:  -3.498
# Rotatable Bonds:  0
TPSA:  111.13
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.362
Synthetic Accessibility Score:  2.471
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.082
MDCK Permeability:  5.92807828070363e-06
Pgp-inhibitor:  0.003
Pgp-substrate:  0.087
Human Intestinal Absorption (HIA):  0.169
20% Bioavailability (F20%):  0.929
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.014
Plasma Protein Binding (PPB):  91.39659881591797%
Volume Distribution (VD):  0.658
Pgp-substrate:  11.575908660888672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.977
CYP1A2-substrate:  0.221
CYP2C19-inhibitor:  0.045
CYP2C19-substrate:  0.049
CYP2C9-inhibitor:  0.501
CYP2C9-substrate:  0.834
CYP2D6-inhibitor:  0.479
CYP2D6-substrate:  0.3
CYP3A4-inhibitor:  0.277
CYP3A4-substrate:  0.058

ADMET: Excretion

Clearance (CL):  9.473
Half-life (T1/2):  0.908

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.074
Drug-inuced Liver Injury (DILI):  0.957
AMES Toxicity:  0.538
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.951
Carcinogencity:  0.033
Eye Corrosion:  0.094
Eye Irritation:  0.951
Respiratory Toxicity:  0.138

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  Natural Product: NPC127296

Natural Product ID:  NPC127296
Common Name*:   DAPUVWUGKNRLJU-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DAPUVWUGKNRLJU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H8O6.C7H14O4/c14-5-1-9(17)12-11(2-5)19-10-4-8(16)7(15)3-6(10)13(12)18;1-2-5-7(10)6(9)4(8)3-11-5/h1-4,14-17H;4-10H,2-3H2,1H3
SMILES:  c1c(cc2c(c1O)c(=O)c1cc(c(cc1o2)O)O)O.CCC1C(C(C(CO1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/hlca.19270100148]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. DOI[10.1246/bcsj.30.618]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Petals n.a. n.a. PMID[15043425]
NPO30734 Belamcanda chinensis Species Iridaceae Eukaryota rhizomes Thai n.a. PMID[15787436]
NPO29953 Bombax malabaricum Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[17764148]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[19645233]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota rhizomes n.a. n.a. PMID[19757853]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. rhizome n.a. PMID[21370894]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[24338885]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. PMID[27466882]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota Rhizomes n.a. n.a. PMID[8482946]
NPO30734 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[9917289]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO703 Hypericum ancherii Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29504 Urena lobata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29953 Bombax malabaricum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24078 Pyrrosia petiolosa Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30734 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1639 Pyrrosia lingua Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15181 Pyrrosia pseudocalvata Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18581 Pyrrosia davidii Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO703 Hypericum ancherii Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18581 Pyrrosia davidii Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24078 Pyrrosia petiolosa Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15181 Pyrrosia pseudocalvata Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29504 Urena lobata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1639 Pyrrosia lingua Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29953 Bombax malabaricum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1639 Pyrrosia lingua Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30734 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24078 Pyrrosia petiolosa Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1639 Pyrrosia lingua Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1639 Pyrrosia lingua Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29504 Urena lobata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29314 Mangifera indica Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18581 Pyrrosia davidii Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13507 Mangifera persiciformis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC127296 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC127296 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data