NPASS Compound

Structure

NPC180104 OpenBabel06302215322D 32 34 0 0 1 0 0 0 0 0999 V2000 -4.2072 3.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0733 3.1691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9393 3.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9393 4.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0733 2.1691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9393 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9393 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6713 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6713 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5374 2.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5374 3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5374 0.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5374 -0.8309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8053 -0.8309 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6713 -1.3309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 1.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 3.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 -0.9135 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 0.1229 2.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9889 1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 6 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 6 7 1 0 0 0 0 6 19 1 6 0 0 0 7 12 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 17 1 0 0 0 0 10 11 2 0 0 0 0 10 15 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 24 31 1 0 0 0 0 25 30 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 31 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	446.16
Volume:	438.715
LogP:	2.936
LogD:	3.11
LogS:	-5.051
# Rotatable Bonds:	10
TPSA:	98.75
# H-Bond Aceptor:	9
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.535
Synthetic Accessibility Score:	3.347
Fsp3:	0.391
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:	-4.681
MDCK Permeability:	3.8352201954694465e-05
Pgp-inhibitor:	0.989
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.201

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.069
Plasma Protein Binding (PPB):	84.96754455566406%
Volume Distribution (VD):	0.604
Pgp-substrate:	15.399296760559082%

ADMET: Metabolism

CYP1A2-inhibitor:	0.11
CYP1A2-substrate:	0.969
CYP2C19-inhibitor:	0.907
CYP2C19-substrate:	0.897
CYP2C9-inhibitor:	0.86
CYP2C9-substrate:	0.862
CYP2D6-inhibitor:	0.56
CYP2D6-substrate:	0.887
CYP3A4-inhibitor:	0.958
CYP3A4-substrate:	0.906

ADMET: Excretion

Clearance (CL):	10.469
Half-life (T1/2):	0.481

ADMET: Toxicity

hERG Blockers:	0.304
Human Hepatotoxicity (H-HT):	0.165
Drug-inuced Liver Injury (DILI):	0.842
AMES Toxicity:	0.022
Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.03
Skin Sensitization:	0.301
Carcinogencity:	0.122
Eye Corrosion:	0.009
Eye Irritation:	0.126
Respiratory Toxicity:	0.078

Download Data

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

Natural Product: NPC180104

Natural Product ID:	NPC180104
*Common Name:**	UMPFZWIPEWEVRH-YUNKPMOVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UMPFZWIPEWEVRH-YUNKPMOVSA-N
Standard InCHI:	InChI=1S/C23H26O9/c1-12(13(2)24)20(14-7-16(26-3)21(29-6)17(8-14)27-4)32-23(25)15-9-18(28-5)22-19(10-15)30-11-31-22/h7-10,12,20H,11H2,1-6H3/t12-,20-/m0/s1
SMILES:	C[C@@H](C(=O)C)[C@@H](c1cc(c(c(c1)OC)OC)OC)OC(=O)c1cc(c2c(c1)OCO2)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11859072
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0001248] Hydroxybenzoic acid derivatives [CHEMONTID:0001251] Gallic acid and derivatives

*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
NPO4331	Plakortis lita	Species	Plakinidae	Eukaryota	n.a.	Palauan	n.a.	PMID[10479343]
NPO4331	Plakortis lita	Species	Plakinidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[11277756]
NPO25126	Sarcophyton latum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16724849]
NPO25126	Sarcophyton latum	Species	Orchidaceae	Eukaryota	n.a.	Hainan soft coral	n.a.	PMID[16724849]
NPO8247	Austrobaileya scandens	Species	Austrobaileyaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27214307]
NPO2861	Pentaceraster regulus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[28981263]
NPO4331	Plakortis lita	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9722494]
NPO569	Micromelum integerrimum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO569	Micromelum integerrimum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5844	Schlumbergera truncata	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO569	Micromelum integerrimum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7401	Centaurea dealbata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO569	Micromelum integerrimum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3331	Hedysarum sachalinense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8247	Austrobaileya scandens	Species	Austrobaileyaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5582	Inocybe aeruginascens	Species	Inocybaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25126	Sarcophyton latum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1462	Amomum sulcatum	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6053	Veronica intercedens	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9215	Papaver glaucum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27884	Sphacelaria arctica	Species	Sphacelariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO772	Bosistoa floydii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4888	Salvia divaricata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2861	Pentaceraster regulus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4331	Plakortis lita	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO345	Quercus laurifolia	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5844	Schlumbergera truncata	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6791	Malva rotundifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6305	Euphorbia jaxartica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO134	Cassia artemisioides	Species	Fabaceae	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 NPC180104 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	411
0.1-0.2	1542
0.2-0.3	3852
0.3-0.4	8466
0.4-0.5	9937
0.5-0.6	3898
0.6-0.7	5679
0.7-0.8	7597
0.8-0.85	1154
0.85-0.9	143
0.9-0.95	15
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 NPC180104 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	340
0.1-0.2	915
0.2-0.3	1854
0.3-0.4	2650
0.4-0.5	1845
0.5-0.6	998
0.6-0.7	398
0.7-0.8	130
0.8-0.85	18
0.85-0.9	1
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