NPASS Compound

Structure

NPC86189 OpenBabel06302215582D 22 24 0 0 0 0 0 0 0 0999 V2000 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 18 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 22 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 21 1 0 0 0 0 6 18 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 9 19 1 0 0 0 0 10 11 1 0 0 0 0 10 17 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	298.08
Volume:	299.778
LogP:	3.57
LogD:	2.95
LogS:	-3.549
# Rotatable Bonds:	2
TPSA:	79.9
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.759
Synthetic Accessibility Score:	2.331
Fsp3:	0.118
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.877
MDCK Permeability:	1.4779592675040476e-05
Pgp-inhibitor:	0.791
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.018
Plasma Protein Binding (PPB):	97.24373626708984%
Volume Distribution (VD):	0.509
Pgp-substrate:	3.7750184535980225%

ADMET: Metabolism

CYP1A2-inhibitor:	0.952
CYP1A2-substrate:	0.864
CYP2C19-inhibitor:	0.659
CYP2C19-substrate:	0.072
CYP2C9-inhibitor:	0.814
CYP2C9-substrate:	0.837
CYP2D6-inhibitor:	0.626
CYP2D6-substrate:	0.255
CYP3A4-inhibitor:	0.434
CYP3A4-substrate:	0.158

ADMET: Excretion

Clearance (CL):	4.25
Half-life (T1/2):	0.722

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.131
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.736
Rat Oral Acute Toxicity:	0.291
Maximum Recommended Daily Dose:	0.126
Skin Sensitization:	0.575
Carcinogencity:	0.306
Eye Corrosion:	0.006
Eye Irritation:	0.905
Respiratory Toxicity:	0.219

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC86189

Natural Product ID:	NPC86189
*Common Name:**	YOLLWVZOKWMPBR-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YOLLWVZOKWMPBR-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C17H14O5/c1-9-11(18)8-12(19)13-14(20)17(21-2)16(22-15(9)13)10-6-4-3-5-7-10/h3-8,18-19H,1-2H3
SMILES:	Cc1c(cc(c2c(=O)c(c(c3ccccc3)oc12)OC)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44258730
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002588] 3-O-methylated flavonoids

*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
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	Vietnamese	n.a.	PMID[11325227]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12542368]
NPO22637	Kunzea ambigua	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15043420]
NPO10407	Petromyzon marinus	Species	Petromyzontidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15193266]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28139925]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31184894]
NPO24672	Helleborus purpurascens	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24672	Helleborus purpurascens	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16885	Phonus arborescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5676	Annulohypoxylon multiforme	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25468	Tabernaemontana amygdalifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19721	Impatiens roylei	Species	Balsaminaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28771	Clematis delavayi	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23489	Stachys anisochila	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24821	Nidorella resedifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22637	Kunzea ambigua	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18950	Cephalotaxus fortunei	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8943	Juniperus californica	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25128	Panax vietnamensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24591	Trichosanthes dioica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25321	Acantholimon glumaceum	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17249	Lespedeza capitata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25557	Alternaria porri	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25410	Manilkara bidentata	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10407	Petromyzon marinus	Species	Petromyzontidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24866	Smilax aspera	Species	Smilacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24549	Scutellaria cordifrons	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24735	Cupania latifolia	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24672	Helleborus purpurascens	Species	Ranunculaceae	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 NPC86189 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	448
0.1-0.2	1925
0.2-0.3	4762
0.3-0.4	11128
0.4-0.5	6517
0.5-0.6	4004
0.6-0.7	5463
0.7-0.8	4143
0.8-0.85	2145
0.85-0.9	1593
0.9-0.95	525
0.95-1	44

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 NPC86189 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	425
0.1-0.2	983
0.2-0.3	1709
0.3-0.4	2669
0.4-0.5	1833
0.5-0.6	1015
0.6-0.7	343
0.7-0.8	101
0.8-0.85	45
0.85-0.9	21
0.9-0.95	5
0.95-1	1

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