NPASS Compound

Structure

NPC238943 OpenBabel06302215432D 57 62 0 0 1 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 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 5.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 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 3.4641 3.0000 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 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 O 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 0.0000 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 7.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 6.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 5.0000 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 -2.5981 0.5000 0.0000 O 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 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 54 1 0 0 0 0 3 4 1 0 0 0 0 3 57 1 6 0 0 0 4 5 1 0 0 0 0 4 56 1 1 0 0 0 5 6 1 0 0 0 0 5 55 1 1 0 0 0 6 7 1 6 0 0 0 6 54 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 53 1 1 0 0 0 11 12 1 0 0 0 0 11 52 1 6 0 0 0 12 13 1 0 0 0 0 12 36 1 1 0 0 0 13 14 1 0 0 0 0 13 15 1 6 0 0 0 15 16 1 0 0 0 0 16 26 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 35 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 34 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 40 2 0 0 0 0 40 41 1 0 0 0 0 41 46 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 43 44 1 0 0 0 0 43 50 1 0 0 0 0 44 45 2 0 0 0 0 44 49 1 0 0 0 0 45 46 1 0 0 0 0 45 47 1 0 0 0 0 47 48 1 0 0 0 0 50 51 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	800.22
Volume:	747.205
LogP:	2.338
LogD:	1.219
LogS:	-3.559
# Rotatable Bonds:	12
TPSA:	293.96
# H-Bond Aceptor:	19
# H-Bond Donor:	9
# Rings:	6
# Heavy Atoms:	19

MedChem Properties

QED Drug-Likeness Score:	0.074
Synthetic Accessibility Score:	5.124
Fsp3:	0.368
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.492
MDCK Permeability:	2.8142721930635162e-05
Pgp-inhibitor:	0.042
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.857
20% Bioavailability (F20%):	0.023
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.025
Plasma Protein Binding (PPB):	91.28231048583984%
Volume Distribution (VD):	0.562
Pgp-substrate:	16.639240264892578%

ADMET: Metabolism

CYP1A2-inhibitor:	0.047
CYP1A2-substrate:	0.135
CYP2C19-inhibitor:	0.046
CYP2C19-substrate:	0.055
CYP2C9-inhibitor:	0.408
CYP2C9-substrate:	0.386
CYP2D6-inhibitor:	0.223
CYP2D6-substrate:	0.165
CYP3A4-inhibitor:	0.144
CYP3A4-substrate:	0.024

ADMET: Excretion

Clearance (CL):	2.621
Half-life (T1/2):	0.873

ADMET: Toxicity

hERG Blockers:	0.196
Human Hepatotoxicity (H-HT):	0.16
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.726
Rat Oral Acute Toxicity:	0.052
Maximum Recommended Daily Dose:	0.063
Skin Sensitization:	0.945
Carcinogencity:	0.062
Eye Corrosion:	0.003
Eye Irritation:	0.154
Respiratory Toxicity:	0.026

Download Data

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

Natural Product: NPC238943

Natural Product ID:	NPC238943
*Common Name:**	ZQDOJGMOEVMUEY-MXAFTYQDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZQDOJGMOEVMUEY-MXAFTYQDSA-N
Standard InCHI:	InChI=1S/C38H40O19/c1-15-27(43)31(47)33(49)37(53-15)52-14-24-29(45)32(48)36(56-25(42)9-4-16-10-22(50-2)28(44)23(11-16)51-3)38(55-24)57-35-30(46)26-20(41)12-19(40)13-21(26)54-34(35)17-5-7-18(39)8-6-17/h4-13,15,24,27,29,31-33,36-41,43-45,47-49H,14H2,1-3H3/b9-4+/t15-,24+,27-,29+,31+,32-,33+,36+,37+,38-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)Oc2c(=O)c3c(cc(cc3oc2c2ccc(cc2)O)O)O)OC(=O)/C=C/c2cc(c(c(c2)OC)O)OC)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101781233
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-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
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota	bud covers	n.a.	n.a.	PMID[11975520]
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[12662107]
NPO5870	Xenia florida	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[16643051]
NPO12386	Russula japonica	Species	Russulaceae	Eukaryota	fruiting body	n.a.	n.a.	PMID[16989517]
NPO20045	Burkholderia cepacia	Species	Burkholderiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[3839140]
NPO20045	Burkholderia cepacia	Species	Burkholderiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[7684040]
NPO5870	Xenia florida	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[9868153]
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO14379	Onobrychis viciifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7731	Lactuca serriola	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14274	Rhododendron mucronatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2469	Erythrophleum couminga	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7731	Lactuca serriola	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14274	Rhododendron mucronatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14379	Onobrychis viciifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2469	Erythrophleum couminga	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2469	Erythrophleum couminga	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14274	Rhododendron mucronatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8171	Artocarpus altilis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13192	Chara ceratophylla	Species	Characeae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10892	Xanthorrhoea resinosa	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16013	Inga velutina	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10594	Centaurea solstitialis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12726	Piptostigma fugax	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12035	Rhododendron ungerni	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5380	Eucalyptus australiana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14274	Rhododendron mucronatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20585	Urochloa decumbens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20045	Burkholderia cepacia	Species	Burkholderiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO16306	Curcuma caesia	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13683	Cosmos diversifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12207	Lagochilus leiacanthus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14075	Streptomyces viridogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9342	Solenopsis punctaticeps	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14379	Onobrychis viciifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO206	Ormosia nobilis	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10928	Xenia obscuronata	Species	Xeniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12386	Russula japonica	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3059	Erythrina pallida	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11046	Ocimum pilosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2046	Cathormion altissimum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO875	Cryptocarya oblata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5870	Xenia florida	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2469	Erythrophleum couminga	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12557	Strychnos tricalysioides	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1398	Trichodesma incanum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7608	Phelline lucida	Species	Phellinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7731	Lactuca serriola	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 NPC238943 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	437
0.1-0.2	1799
0.2-0.3	4061
0.3-0.4	9037
0.4-0.5	8868
0.5-0.6	5044
0.6-0.7	5666
0.7-0.8	5263
0.8-0.85	1511
0.85-0.9	474
0.9-0.95	435
0.95-1	102

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 NPC238943 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	393
0.1-0.2	959
0.2-0.3	2060
0.3-0.4	2661
0.4-0.5	1852
0.5-0.6	821
0.6-0.7	266
0.7-0.8	99
0.8-0.85	24
0.85-0.9	7
0.9-0.95	6
0.95-1	2

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