NPASS Compound

Structure

NPC12947 OpenBabel06302215272D 25 26 0 0 1 0 0 0 0 0999 V2000 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 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 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 1 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 0.8660 -1.5000 0.0000 C 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 -0.8660 -1.5000 0.0000 C 0 0 0 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 -3.0000 0.0000 O 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 -2.5981 -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 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 O 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 -3.0000 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 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 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 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 25 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 21 1 0 0 0 0 6 17 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 9 16 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	344.13
Volume:	351.717
LogP:	4.121
LogD:	2.973
LogS:	-3.139
# Rotatable Bonds:	5
TPSA:	96.22
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.337
Synthetic Accessibility Score:	3.233
Fsp3:	0.211
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:	-5.018
MDCK Permeability:	2.010187199630309e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.187
Human Intestinal Absorption (HIA):	0.487
20% Bioavailability (F20%):	0.937
30% Bioavailability (F30%):	0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.017
Plasma Protein Binding (PPB):	97.14759063720703%
Volume Distribution (VD):	0.685
Pgp-substrate:	7.943737506866455%

ADMET: Metabolism

CYP1A2-inhibitor:	0.964
CYP1A2-substrate:	0.869
CYP2C19-inhibitor:	0.299
CYP2C19-substrate:	0.078
CYP2C9-inhibitor:	0.733
CYP2C9-substrate:	0.919
CYP2D6-inhibitor:	0.787
CYP2D6-substrate:	0.692
CYP3A4-inhibitor:	0.131
CYP3A4-substrate:	0.215

ADMET: Excretion

Clearance (CL):	2.811
Half-life (T1/2):	0.784

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.051
Drug-inuced Liver Injury (DILI):	0.476
AMES Toxicity:	0.482
Rat Oral Acute Toxicity:	0.854
Maximum Recommended Daily Dose:	0.589
Skin Sensitization:	0.928
Carcinogencity:	0.274
Eye Corrosion:	0.364
Eye Irritation:	0.959
Respiratory Toxicity:	0.267

Download Data

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

Natural Product: NPC12947

Natural Product ID:	NPC12947
*Common Name:**	SCIUCADXFKAPEB-INIZCTEOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SCIUCADXFKAPEB-INIZCTEOSA-N
Standard InCHI:	InChI=1S/C19H20O6/c1-10(2)5-8-16(25-11(3)20)12-9-15(23)17-13(21)6-7-14(22)18(17)19(12)24-4/h5-7,9,16,23H,8H2,1-4H3/t16-/m0/s1
SMILES:	CC(=CC[C@@H](c1cc(c2C(=O)C=CC(=O)c2c1OC)O)OC(=O)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	157629
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000023] Naphthalenes [CHEMONTID:0000153] Naphthoquinones

*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
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	roots	n.a.	n.a.	PMID[10217724]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12398531]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12502328]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17488128]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19534474]
NPO20181	Dracaena arborea	Species	Asparagaceae	Eukaryota	bark	Yaound, village of Bangoua, near Bangangt	2007-APR	PMID[20553003]
NPO5119.1	Pseudomonas chlororaphis subsp. aurantiaca	Subspecies	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[31999458]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7775984]
NPO19871	Rubus arcticus	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18550	Teucrium gnaphalodes	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14913	Robinia neomexicana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19789	Umbilicaria polyphylla	Species	Umbilicariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18713	Strychnos usambarensis	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19871	Rubus arcticus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11300	Eucalyptus coccifera	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9209	Rhizomnium magnifolium	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20181	Dracaena arborea	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5119.1	Pseudomonas chlororaphis subsp. aurantiaca	Subspecies	Pseudomonadaceae	Bacteria	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 NPC12947 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	333
0.1-0.2	1426
0.2-0.3	3473
0.3-0.4	7714
0.4-0.5	10823
0.5-0.6	4131
0.6-0.7	6756
0.7-0.8	7012
0.8-0.85	891
0.85-0.9	130
0.9-0.95	8
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 NPC12947 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	292
0.1-0.2	950
0.2-0.3	1592
0.3-0.4	2464
0.4-0.5	2023
0.5-0.6	1170
0.6-0.7	457
0.7-0.8	186
0.8-0.85	12
0.85-0.9	4
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