NPASS Compound

Structure

NPC130391 OpenBabel06302216102D 27 31 0 0 1 0 0 0 0 0999 V2000 -3.9346 -1.2045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9346 -0.2045 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9836 0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5768 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5823 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3958 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3958 1.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9836 2.7226 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.3958 3.5316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9346 3.0316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8857 2.7226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4735 1.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3395 2.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2055 1.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2055 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3395 0.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4735 0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8857 0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4735 -0.7045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1566 0.6045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7444 1.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1566 2.2226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6581 1.4781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2079 0.9781 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 20 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 27 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 25 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 24 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	367.14
Volume:	365.483
LogP:	3.644
LogD:	2.743
LogS:	-5.191
# Rotatable Bonds:	0
TPSA:	57.23
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.713
Synthetic Accessibility Score:	3.686
Fsp3:	0.381
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.1
MDCK Permeability:	2.7713831514120102e-05
Pgp-inhibitor:	0.105
Pgp-substrate:	0.032
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.927
Plasma Protein Binding (PPB):	96.3294906616211%
Volume Distribution (VD):	2.329
Pgp-substrate:	3.391061305999756%

ADMET: Metabolism

CYP1A2-inhibitor:	0.949
CYP1A2-substrate:	0.482
CYP2C19-inhibitor:	0.937
CYP2C19-substrate:	0.904
CYP2C9-inhibitor:	0.103
CYP2C9-substrate:	0.825
CYP2D6-inhibitor:	0.978
CYP2D6-substrate:	0.927
CYP3A4-inhibitor:	0.97
CYP3A4-substrate:	0.864

ADMET: Excretion

Clearance (CL):	14.504
Half-life (T1/2):	0.122

ADMET: Toxicity

hERG Blockers:	0.767
Human Hepatotoxicity (H-HT):	0.238
Drug-inuced Liver Injury (DILI):	0.814
AMES Toxicity:	0.4
Rat Oral Acute Toxicity:	0.445
Maximum Recommended Daily Dose:	0.832
Skin Sensitization:	0.167
Carcinogencity:	0.72
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.919

Download Data

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

Natural Product: NPC130391

Natural Product ID:	NPC130391
*Common Name:**	WOLWLEQYUFDNTA-GFCCVEGCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WOLWLEQYUFDNTA-GFCCVEGCSA-N
Standard InCHI:	InChI=1S/C21H21NO5/c1-12-14-3-4-17-21(27-11-24-17)16(14)9-22(2)6-5-13-7-18-19(26-10-25-18)8-15(13)20(12)23/h3-4,7-8,12H,5-6,9-11H2,1-2H3/t12-/m1/s1
SMILES:	C[C@@H]1c2ccc3c(c2CN(C)CCc2cc4c(cc2C1=O)OCO4)OCO3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12304036
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002743] Protopine 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
NPO29263	Tylopilus plumbeoviolaceus	Species	Boletaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[10785434]
NPO28926	Corydalis tuberosa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28926	Corydalis tuberosa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29206	Lycopodium chinense	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28926	Corydalis tuberosa	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29347	Hydnum aurantiacum	Species	Hydnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17311	Penicillium vulpinum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29441	Eremophila oppositifolia	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29490	Taxillus yadoriki	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29086	Dovyalis hebecarpa	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29246	Ixeris repens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29263	Tylopilus plumbeoviolaceus	Species	Boletaceae	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 NPC130391 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	310
0.1-0.2	1533
0.2-0.3	5117
0.3-0.4	12179
0.4-0.5	4506
0.5-0.6	10473
0.6-0.7	7768
0.7-0.8	732
0.8-0.85	64
0.85-0.9	9
0.9-0.95	2
0.95-1	4

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 NPC130391 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	755
0.2-0.3	998
0.3-0.4	2028
0.4-0.5	2608
0.5-0.6	1786
0.6-0.7	672
0.7-0.8	87
0.8-0.85	6
0.85-0.9	2
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