NPASS Compound

Structure

NPC195181 OpenBabel06302215552D 32 37 0 0 1 0 0 0 0 0999 V2000 1.8625 5.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6942 4.3005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8628 3.8204 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 1.8627 2.8599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0313 2.3798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0313 1.4195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1997 0.9393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6320 1.4195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6320 2.3798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1997 2.8599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1996 3.8199 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0310 4.3001 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0311 5.2605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1992 5.7405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6323 5.2604 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6320 4.3001 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4636 3.8198 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3931 4.0613 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0669 3.3772 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9964 3.6187 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2519 4.5443 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5781 5.2285 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8337 6.1542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7631 6.3956 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6486 4.9870 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1814 4.7858 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6702 2.9345 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8113 2.4515 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4809 5.7501 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3456 0.7769 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9550 -0.1004 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 13 1 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 32 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 30 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 16 1 0 0 0 0 12 13 1 1 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 29 1 1 0 0 0 16 17 1 6 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 30 31 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	449.17
Volume:	417.292
LogP:	-0.169
LogD:	-0.159
LogS:	-1.558
# Rotatable Bonds:	3
TPSA:	141.31
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.349
Synthetic Accessibility Score:	4.797
Fsp3:	0.636
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:	-5.822
MDCK Permeability:	4.319971412769519e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	0.315
Human Intestinal Absorption (HIA):	0.49
20% Bioavailability (F20%):	0.069
30% Bioavailability (F30%):	0.725

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.278
Plasma Protein Binding (PPB):	58.027915954589844%
Volume Distribution (VD):	0.383
Pgp-substrate:	40.82829666137695%

ADMET: Metabolism

CYP1A2-inhibitor:	0.053
CYP1A2-substrate:	0.123
CYP2C19-inhibitor:	0.021
CYP2C19-substrate:	0.695
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.11
CYP2D6-inhibitor:	0.268
CYP2D6-substrate:	0.233
CYP3A4-inhibitor:	0.026
CYP3A4-substrate:	0.124

ADMET: Excretion

Clearance (CL):	2.872
Half-life (T1/2):	0.809

ADMET: Toxicity

hERG Blockers:	0.023
Human Hepatotoxicity (H-HT):	0.163
Drug-inuced Liver Injury (DILI):	0.164
AMES Toxicity:	0.501
Rat Oral Acute Toxicity:	0.428
Maximum Recommended Daily Dose:	0.496
Skin Sensitization:	0.043
Carcinogencity:	0.883
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.736

Download Data

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

Natural Product: NPC195181

Natural Product ID:	NPC195181
*Common Name:**	NVHVNOCMXAHWMA-JXXVXVCISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NVHVNOCMXAHWMA-JXXVXVCISA-N
Standard InCHI:	InChI=1S/C22H27NO9/c24-7-15-18(26)19(27)20(28)22(31-15)32-21-12(25)3-9-1-2-23-6-10-4-13-14(30-8-29-13)5-11(10)16(21)17(9)23/h3-5,12,15-22,24-28H,1-2,6-8H2/t12-,15+,16-,17+,18+,19-,20+,21+,22-/m0/s1
SMILES:	C1CN2Cc3cc4c(cc3[C@H]3[C@H]2C1=C[C@@H]([C@H]3O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)OCO4
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001775] Amaryllidaceae alkaloids [CHEMONTID:0004120] Lycorine-type amaryllidaceae alkaloids

*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
NPO13784	Dalbergia candenatensis	Species	Fabaceae	Eukaryota	heartwood	n.a.	n.a.	PMID[19653666]
NPO12711	Ligularia altaica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20073490]
NPO4576	Corynandra viscosa	Species	Cleomaceae	Eukaryota	n.a.	leaf	n.a.	PMID[28135851]
NPO13784	Dalbergia candenatensis	Species	Fabaceae	Eukaryota	n.a.	Thai	n.a.	PMID[3430167]
NPO3630	Crotalaria crispata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9927	Crinum asiaticum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4576	Corynandra viscosa	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9927	Crinum asiaticum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3630	Crotalaria crispata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12711	Ligularia altaica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10319	Calycodendron milnei	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13784	Dalbergia candenatensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9612	Dryopteris dilatata	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3630	Crotalaria crispata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4576	Corynandra viscosa	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9927	Crinum asiaticum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1412	Artemisia juncea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19776	Hesperocyparis arizonica	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11000	Eupatorium laevigatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11473	Viburnum lantana	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25680	Ramalina siliquosa	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9485	Haplopappus deserticola	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9144	Atriplex parvifolia	Species	Chenopodiaceae	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 NPC195181 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	331
0.1-0.2	1296
0.2-0.3	3589
0.3-0.4	10320
0.4-0.5	9700
0.5-0.6	11784
0.6-0.7	4494
0.7-0.8	1034
0.8-0.85	76
0.85-0.9	58
0.9-0.95	15
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 NPC195181 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	187
0.1-0.2	641
0.2-0.3	892
0.3-0.4	2477
0.4-0.5	2676
0.5-0.6	1614
0.6-0.7	556
0.7-0.8	100
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