NPASS Compound

Structure

NPC228834 OpenBabel06302215502D 32 35 0 0 1 0 0 0 0 0999 V2000 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 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 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 -1.7321 1.0000 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 -1.7321 -0.0000 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 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -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 -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 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 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 3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 32 1 0 0 0 0 4 5 2 0 0 0 0 4 31 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 30 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 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 12 30 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 29 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 25 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 6 0 0 0 20 21 1 0 0 0 0 20 27 1 1 0 0 0 21 22 1 0 0 0 0 21 26 1 6 0 0 0 22 23 1 1 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	510.17
Volume:	479.098
LogP:	0.465
LogD:	0.813
LogS:	-2.593
# Rotatable Bonds:	7
TPSA:	176.76
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.285
Synthetic Accessibility Score:	4.265
Fsp3:	0.5
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.468
MDCK Permeability:	3.384862429811619e-05
Pgp-inhibitor:	0.02
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.541
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.862

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.272
Plasma Protein Binding (PPB):	60.6586799621582%
Volume Distribution (VD):	0.59
Pgp-substrate:	35.993011474609375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.563
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.796
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.538
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.281
CYP3A4-inhibitor:	0.021
CYP3A4-substrate:	0.178

ADMET: Excretion

Clearance (CL):	6.015
Half-life (T1/2):	0.687

ADMET: Toxicity

hERG Blockers:	0.283
Human Hepatotoxicity (H-HT):	0.26
Drug-inuced Liver Injury (DILI):	0.047
AMES Toxicity:	0.088
Rat Oral Acute Toxicity:	0.026
Maximum Recommended Daily Dose:	0.108
Skin Sensitization:	0.517
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC228834

Natural Product ID:	NPC228834
*Common Name:**	KBGKQZVCLWKUDQ-QNDFHXLGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KBGKQZVCLWKUDQ-QNDFHXLGSA-N
Standard InCHI:	InChI=1S/C21H20O11/c22-7-16-18(27)19(28)20(29)21(32-16)31-15-5-9(23)4-14-17(15)12(26)6-13(30-14)8-1-2-10(24)11(25)3-8/h1-6,16,18-25,27-29H,7H2/t16-,18-,19+,20-,21-/m1/s1
SMILES:	c1cc(c(cc1c1cc(=O)c2c(cc(cc2O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)o1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5317471
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides

*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
NPO3171	Menisporopsis theobromae	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	PMID[15104506]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919095]
NPO6350	Spongia officinalis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21548580]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	flower	n.a.	PMID[21916433]
NPO5813	Ligularia songarica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23043462]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	flower buds and leaves	Khon Kaen province, Thailand	2010	PMID[23270663]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[23558238]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[23642481]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24195447]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	Gum resin	n.a.	n.a.	PMID[26457560]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[26462418]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27228307]
NPO6350	Spongia officinalis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[31095383]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO21528	Equisetum arvense	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14881	Senecio nemorensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21528	Equisetum arvense	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14881	Senecio nemorensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26001	Carlina acaulis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21528	Equisetum arvense	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14881	Senecio nemorensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22231	Fagara naranjillo	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO735	Pteraster multipes	Species	Pterasteridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21528	Equisetum arvense	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4783	Cyphus niveus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO5813	Ligularia songarica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5007	Deltocyathus magnificus	Species	Caryophylliidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3171	Menisporopsis theobromae	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO460	Alangium ridleyi	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO392	Laurencia composita	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22430	Parnassius phoebus	Species	Papilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4658	Hedysarum denticulatum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6350	Spongia officinalis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20516	Hydrocotyle ranunculoides	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28795	Retiboletus ornatipes	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3319	Helichrysum nitens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20196	Aplysia vaccaria	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26001	Carlina acaulis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14881	Senecio nemorensis	Species	Asteraceae	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 NPC228834 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	445
0.1-0.2	1835
0.2-0.3	4139
0.3-0.4	9743
0.4-0.5	8335
0.5-0.6	4113
0.6-0.7	5112
0.7-0.8	5204
0.8-0.85	1975
0.85-0.9	1251
0.9-0.95	404
0.95-1	141

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 NPC228834 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	414
0.1-0.2	929
0.2-0.3	1905
0.3-0.4	2694
0.4-0.5	1797
0.5-0.6	934
0.6-0.7	295
0.7-0.8	135
0.8-0.85	20
0.85-0.9	17
0.9-0.95	9
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