NPASS Compound

Structure

NPC119376 OpenBabel06302216172D 27 31 0 0 1 0 0 0 0 0999 V2000 2.5823 0.7045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5878 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3090 -0.9511 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2601 -1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4680 -2.2382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4190 -2.5472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6270 -3.5254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8838 -4.1945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9328 -3.8855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7248 -2.9074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3450 -4.6945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9328 -5.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8838 -5.1945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5000 -2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3660 -3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3660 -4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2321 -4.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0981 -4.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0981 -3.0388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2321 -2.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0491 -2.7298 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6369 -3.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0491 -4.3479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 27 1 0 0 0 0 4 5 1 6 0 0 0 4 15 1 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 14 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 1 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 17 22 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 25 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	370.14
Volume:	365.912
LogP:	4.249
LogD:	3.283
LogS:	-5.557
# Rotatable Bonds:	5
TPSA:	55.38
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.806
Synthetic Accessibility Score:	3.578
Fsp3:	0.429
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.968
MDCK Permeability:	3.7462847103597596e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.112
Plasma Protein Binding (PPB):	99.15821075439453%
Volume Distribution (VD):	0.631
Pgp-substrate:	1.5545377731323242%

ADMET: Metabolism

CYP1A2-inhibitor:	0.904
CYP1A2-substrate:	0.234
CYP2C19-inhibitor:	0.966
CYP2C19-substrate:	0.291
CYP2C9-inhibitor:	0.73
CYP2C9-substrate:	0.637
CYP2D6-inhibitor:	0.991
CYP2D6-substrate:	0.922
CYP3A4-inhibitor:	0.978
CYP3A4-substrate:	0.793

ADMET: Excretion

Clearance (CL):	16.805
Half-life (T1/2):	0.237

ADMET: Toxicity

hERG Blockers:	0.62
Human Hepatotoxicity (H-HT):	0.298
Drug-inuced Liver Injury (DILI):	0.89
AMES Toxicity:	0.173
Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.683
Skin Sensitization:	0.836
Carcinogencity:	0.906
Eye Corrosion:	0.003
Eye Irritation:	0.161
Respiratory Toxicity:	0.431

Download Data

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

Natural Product: NPC119376

Natural Product ID:	NPC119376
*Common Name:**	UUUXPUGZNDRYSV-MRUHUIDDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UUUXPUGZNDRYSV-MRUHUIDDSA-N
Standard InCHI:	InChI=1S/C21H22O6/c1-22-21-16(7-14-3-5-18-20(9-14)27-12-25-18)15(10-23-21)6-13-2-4-17-19(8-13)26-11-24-17/h2-5,8-9,15-16,21H,6-7,10-12H2,1H3/t15-,16+,21-/m0/s1
SMILES:	CO[C@@H]1[C@H](Cc2ccc3c(c2)OCO3)[C@@H](Cc2ccc3c(c2)OCO3)CO1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101690800
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003424] 9,9'-epoxylignans

*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
NPO8246	Lantana involucrata	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15217280]
NPO8188	Hypoestes purpurea	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15568798]
NPO4890	Streptomyces rimosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17631493]
NPO13607	Arenaria kansuensis	Species	Scolopacidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17655145]
NPO4890	Streptomyces rimosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1833366]
NPO9032	Geotrichum candidum	Species	Dipodascaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20488699]
NPO13305	Mammea africana	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8188	Hypoestes purpurea	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14190	Streptopelia orientalis	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13607	Arenaria kansuensis	Species	Scolopacidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14190	Streptopelia orientalis	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13305	Mammea africana	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8188	Hypoestes purpurea	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6089	Metacalypogeia alternifolia	Species	Calypogeiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9032	Geotrichum candidum	Species	Dipodascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11341	Eucalyptus piperita	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13497	Senecio trichopterygius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8246	Lantana involucrata	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13201	Diphasiastrum tristachyum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14882	Collariella gracilis	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13607	Arenaria kansuensis	Species	Scolopacidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14190	Streptopelia orientalis	Species	Columbidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7350	Sitotroga cerealella	Species	Gelechiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8655	Wendlandia tinctoria	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13305	Mammea africana	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7119	Endospermum diadenum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5412	Tedania anhelans	Species	Tedaniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8188	Hypoestes purpurea	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2510	Pteris argentea	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4890	Streptomyces rimosus	Species	Streptomycetaceae	Bacteria	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 NPC119376 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	442
0.1-0.2	1476
0.2-0.3	3870
0.3-0.4	12280
0.4-0.5	6854
0.5-0.6	8930
0.6-0.7	6459
0.7-0.8	1989
0.8-0.85	240
0.85-0.9	117
0.9-0.95	35
0.95-1	5

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 NPC119376 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	346
0.1-0.2	871
0.2-0.3	1566
0.3-0.4	2856
0.4-0.5	1859
0.5-0.6	1111
0.6-0.7	457
0.7-0.8	82
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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