NPASS Compound

Structure

NPC138161 OpenBabel06302215102D 41 46 0 0 0 0 0 0 0 0999 V2000 1.7321 -3.0000 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 0.8660 -1.5000 0.0000 C 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 2.5981 -0.5000 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 3.4641 -0.0000 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 2.5981 1.5000 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 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 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 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 2.5000 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 2.5000 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 -3.4641 1.0000 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 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 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 -5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 O 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 -2.5981 -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 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 40 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 9 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 40 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 38 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 28 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 30 36 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 38 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 33 35 2 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 38 39 2 0 0 0 0 40 41 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	550.13
Volume:	547.618
LogP:	6.533
LogD:	2.823
LogS:	-9.003
# Rotatable Bonds:	4
TPSA:	136.43
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.308
Synthetic Accessibility Score:	2.807
Fsp3:	0.125
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.958
MDCK Permeability:	5.8488665672484785e-05
Pgp-inhibitor:	0.903
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.213
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	98.98763275146484%
Volume Distribution (VD):	0.228
Pgp-substrate:	0.9320921301841736%

ADMET: Metabolism

CYP1A2-inhibitor:	0.612
CYP1A2-substrate:	0.903
CYP2C19-inhibitor:	0.489
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.441
CYP2C9-substrate:	0.603
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.179
CYP3A4-inhibitor:	0.295
CYP3A4-substrate:	0.159

ADMET: Excretion

Clearance (CL):	5.999
Half-life (T1/2):	0.014

ADMET: Toxicity

hERG Blockers:	0.086
Human Hepatotoxicity (H-HT):	0.091
Drug-inuced Liver Injury (DILI):	0.956
AMES Toxicity:	0.557
Rat Oral Acute Toxicity:	0.751
Maximum Recommended Daily Dose:	0.985
Skin Sensitization:	0.076
Carcinogencity:	0.959
Eye Corrosion:	0.003
Eye Irritation:	0.921
Respiratory Toxicity:	0.029

Download Data

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

Natural Product: NPC138161

Natural Product ID:	NPC138161
*Common Name:**	HVUHXNVQSAMKTQ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HVUHXNVQSAMKTQ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C32H22O9/c1-13-5-17-25(21(33)7-13)31(37)27-19(29(17)35)9-15(11-23(27)39-3)41-16-10-20-28(24(12-16)40-4)32(38)26-18(30(20)36)6-14(2)8-22(26)34/h5-12,33-34H,1-4H3
SMILES:	Cc1cc2c(c(c1)O)C(=O)c1c(cc(cc1OC)Oc1cc3c(c(c1)OC)C(=O)c1c(cc(C)cc1O)C3=O)C2=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	53309223
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones

*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
NPO7198	Scilla socialis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17536859]
NPO2603	Lactuca plumieri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8780	Melicope triphylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10120	Nuxia floribunda	Species	Stilbaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5070	Mycocepurus goeldii	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5575	Parmelia alpicola	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4111	Schistostephium artemisiifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4511	Canarium bengalense	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2779	Syzygium australe	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3524	Endothia longirostris	Species	Cryphonectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9987	Tricholomopsis rutilans	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7834	Tricholoma portentosum	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2417	Xylaria longiana	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8156.1	Taraxacum platycarpum subsp. hondoense	Subspecies	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25664	Halorhodospira halochloris	Species	Ectothiorhodospiraceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO7644	Dysoxylum muelleri	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7198	Scilla socialis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9082	Phialophora asteris	Species	n.a.	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 NPC138161 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	440
0.1-0.2	1810
0.2-0.3	4163
0.3-0.4	10171
0.4-0.5	8154
0.5-0.6	3748
0.6-0.7	5506
0.7-0.8	5402
0.8-0.85	2365
0.85-0.9	807
0.9-0.95	128
0.95-1	3

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 NPC138161 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	398
0.1-0.2	1028
0.2-0.3	1628
0.3-0.4	2671
0.4-0.5	1855
0.5-0.6	1010
0.6-0.7	356
0.7-0.8	158
0.8-0.85	37
0.85-0.9	8
0.9-0.95	1
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