NPASS Compound

Structure

NPC237002 OpenBabel06302216012D 33 35 0 0 1 0 0 0 0 0999 V2000 0.0000 -2.0000 0.0000 C 0 0 0 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 0.8660 -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 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 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0981 0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 1 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 1.7321 -1.0000 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 2.5981 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0981 -1.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 19 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 21 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 20 1 0 0 0 0 7 19 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 17 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 18 19 1 0 0 0 0 21 22 1 0 0 0 0 21 24 1 0 0 0 0 21 33 1 1 0 0 0 22 23 2 0 0 0 0 24 25 1 0 0 0 0 24 32 1 1 0 0 0 25 26 1 0 0 0 0 25 31 1 6 0 0 0 26 27 1 0 0 0 0 26 30 1 6 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	460.1
Volume:	433.727
LogP:	0.549
LogD:	0.192
LogS:	-2.42
# Rotatable Bonds:	8
TPSA:	194.96
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.139
Synthetic Accessibility Score:	4.187
Fsp3:	0.227
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.97
MDCK Permeability:	0.00025747742620296776
Pgp-inhibitor:	0.002
Pgp-substrate:	0.996
Human Intestinal Absorption (HIA):	0.683
20% Bioavailability (F20%):	0.587
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	77.74929809570312%
Volume Distribution (VD):	1.453
Pgp-substrate:	15.33671760559082%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.51
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.152
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.037
CYP3A4-inhibitor:	0.063
CYP3A4-substrate:	0.114

ADMET: Excretion

Clearance (CL):	2.447
Half-life (T1/2):	0.327

ADMET: Toxicity

hERG Blockers:	0.068
Human Hepatotoxicity (H-HT):	0.163
Drug-inuced Liver Injury (DILI):	0.949
AMES Toxicity:	0.4
Rat Oral Acute Toxicity:	0.072
Maximum Recommended Daily Dose:	0.126
Skin Sensitization:	0.086
Carcinogencity:	0.033
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.341

Download Data

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

Natural Product: NPC237002

Natural Product ID:	NPC237002
*Common Name:**	OBVZFHXNNMIIRJ-HBCLNWRISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OBVZFHXNNMIIRJ-HBCLNWRISA-N
Standard InCHI:	InChI=1S/C22H20O11/c1-32-18-11(22(31,9-23)20(28)16(26)17(27)21(29)30)7-12(24)15-13(25)8-14(33-19(15)18)10-5-3-2-4-6-10/h2-9,16-17,20,24,26-28,31H,1H3,(H,29,30)/t16-,17+,20+,22-/m1/s1
SMILES:	COc1c(cc(c2c(=O)cc(c3ccccc3)oc12)O)[C@](C=O)([C@H]([C@@H]([C@@H](C(=O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	29927693
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002593] 8-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
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16755060]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17156960]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[17666848]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[18239311]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19785430]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19829679]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19962306]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20078074]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	root	n.a.	PMID[21087019]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22314230]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23521110]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	whole plants	Nanning District, Guangxi Province, China	2012-Sep	PMID[25647077]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	aerial parts	Seoul, Korea	n.a.	PMID[26331882]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26422318]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28218000]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9834167]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25459	Scutellaria rehderiana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13473	Anodendron affine	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21524	Scutellaria hypericifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13167	Scutellaria amoena	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5431	Scutellaria likiangensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13473	Anodendron affine	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13167	Scutellaria amoena	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25459	Scutellaria rehderiana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5431	Scutellaria likiangensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21524	Scutellaria hypericifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9655	Radix adenophorae	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21524	Scutellaria hypericifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13167	Scutellaria amoena	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5431	Scutellaria likiangensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25459	Scutellaria rehderiana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21387	Forsythia suspensa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16039	Scutellaria barbata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13473	Anodendron affine	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19994	Scutellaria viscidula	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5431	Scutellaria likiangensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25459	Scutellaria rehderiana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13167	Scutellaria amoena	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28877	Scutellaria baicalensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21524	Scutellaria hypericifolia	Species	Lamiaceae	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 NPC237002 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	416
0.1-0.2	1780
0.2-0.3	4367
0.3-0.4	9662
0.4-0.5	8603
0.5-0.6	4086
0.6-0.7	5659
0.7-0.8	5136
0.8-0.85	2094
0.85-0.9	873
0.9-0.95	21
0.95-1	0

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 NPC237002 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	387
0.1-0.2	967
0.2-0.3	2000
0.3-0.4	2609
0.4-0.5	1842
0.5-0.6	892
0.6-0.7	292
0.7-0.8	117
0.8-0.85	35
0.85-0.9	9
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