NPASS Compound

Structure

NPC85985 OpenBabel06302215582D 32 37 0 0 1 0 0 0 0 0999 V2000 5.9290 3.1898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0940 2.7079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0937 1.7439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9285 1.2616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7636 1.7434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7638 2.7075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6399 3.2130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5157 2.7070 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.3918 3.2125 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 10.2676 2.7066 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 10.2674 1.6951 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.3913 1.1896 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 9.3910 0.1782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2668 -0.3278 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5155 1.6956 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.1432 1.1892 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.1437 3.2121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3921 4.2240 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9283 0.2969 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0934 -0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2581 0.2973 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5878 0.2976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7523 -0.1843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9175 0.2979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9177 1.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7527 1.7445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5880 1.2623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4230 1.7442 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2583 1.2619 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0003 1.5609 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5669 0.7806 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 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 29 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 19 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 15 1 0 0 0 0 9 10 1 0 0 0 0 9 18 1 0 0 0 0 10 11 1 0 0 0 0 10 17 1 1 0 0 0 11 12 1 0 0 0 0 11 16 1 6 0 0 0 12 13 1 0 0 0 0 12 15 1 0 0 0 0 13 14 1 0 0 0 0 19 20 1 0 0 0 0 21 20 1 1 0 0 0 21 22 1 0 0 0 0 21 29 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 32 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 30 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 29 28 1 1 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	446.12
Volume:	409.813
LogP:	0.776
LogD:	1.483
LogS:	-4.187
# Rotatable Bonds:	3
TPSA:	136.3
# H-Bond Aceptor:	10
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.518
Synthetic Accessibility Score:	4.269
Fsp3:	0.455
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-6.056
MDCK Permeability:	3.288228981546126e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.181
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.1
Plasma Protein Binding (PPB):	94.67643737792969%
Volume Distribution (VD):	0.615
Pgp-substrate:	4.3759565353393555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.059
CYP1A2-substrate:	0.404
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.687
CYP2C9-inhibitor:	0.038
CYP2C9-substrate:	0.602
CYP2D6-inhibitor:	0.807
CYP2D6-substrate:	0.289
CYP3A4-inhibitor:	0.805
CYP3A4-substrate:	0.308

ADMET: Excretion

Clearance (CL):	3.509
Half-life (T1/2):	0.155

ADMET: Toxicity

hERG Blockers:	0.088
Human Hepatotoxicity (H-HT):	0.736
Drug-inuced Liver Injury (DILI):	0.661
AMES Toxicity:	0.928
Rat Oral Acute Toxicity:	0.053
Maximum Recommended Daily Dose:	0.301
Skin Sensitization:	0.155
Carcinogencity:	0.902
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.043

Download Data

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

Natural Product: NPC85985

Natural Product ID:	NPC85985
*Common Name:**	VGSYCWGXBYZLLE-NEVVRMFVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VGSYCWGXBYZLLE-NEVVRMFVSA-N
Standard InCHI:	InChI=1S/C22H22O10/c23-6-17-18(24)19(25)20(26)22(32-17)30-9-1-2-10-13(3-9)27-7-12-11-4-15-16(29-8-28-15)5-14(11)31-21(10)12/h1-5,12,17-26H,6-8H2/t12-,17?,18+,19-,20?,21-,22+/m0/s1
SMILES:	c1cc2c(cc1O[C@H]1C([C@H]([C@@H](C(CO)O1)O)O)O)OC[C@H]1c3cc4c(cc3O[C@@H]21)OCO4
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44257441
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002617] Furanoisoflavonoids [CHEMONTID:0001608] Pterocarpans

*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
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(00)94679-X]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10869194]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18409045]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[18588343]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19331340]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[19926279]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[2092947]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	berry	n.a.	n.a.	PMID[21216145]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[21911291]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24290061]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24968750]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25152999]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	stems-leaves	n.a.	n.a.	PMID[26420067]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27700077]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[27914541]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28225280]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[28345906]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30199256]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31675225]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31789520]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31804070]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129622]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	kernel	n.a.	PMID[7092570]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10713	Trifolium repens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28300	Sorbaria arborea	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20144	Lespedeza tomentosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1639	Pyrrosia lingua	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27572	Sophora subprostrata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6996	Rubus hirsutus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO6996	Rubus hirsutus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27572	Sophora subprostrata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20144	Lespedeza tomentosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10713	Trifolium repens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28300	Sorbaria arborea	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1639	Pyrrosia lingua	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28300	Sorbaria arborea	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29141	Panax ginseng	Species	Araliaceae	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]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27572	Sophora subprostrata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10713	Trifolium repens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1639	Pyrrosia lingua	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28300	Sorbaria arborea	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1639	Pyrrosia lingua	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6996	Rubus hirsutus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14992	Prunus persica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27572	Sophora subprostrata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20144	Lespedeza tomentosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14112	Uncaria rhynchophylla	Species	Rubiaceae	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 NPC85985 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	474
0.1-0.2	1595
0.2-0.3	4131
0.3-0.4	10304
0.4-0.5	8268
0.5-0.6	4799
0.6-0.7	7433
0.7-0.8	4510
0.8-0.85	826
0.85-0.9	286
0.9-0.95	70
0.95-1	1

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 NPC85985 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	382
0.1-0.2	841
0.2-0.3	1923
0.3-0.4	2818
0.4-0.5	1660
0.5-0.6	916
0.6-0.7	509
0.7-0.8	94
0.8-0.85	7
0.85-0.9	0
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