NPASS Compound

Structure

NPC123557 OpenBabel06302215482D 31 33 0 0 0 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 -4.3301 0.5000 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 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 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 O 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 -0.8660 -1.5000 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 -0.8660 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 0.0000 3.0000 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 1.7321 2.0000 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 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 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 O 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 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 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 O 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 1.7321 3.0000 0.0000 O 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 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 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 5 12 1 0 0 0 0 6 7 2 0 0 0 0 6 11 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 12 22 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 30 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 29 1 0 0 0 0 18 19 1 0 0 0 0 18 27 1 0 0 0 0 19 20 2 0 0 0 0 19 25 1 0 0 0 0 20 21 1 0 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	434.12
Volume:	412.913
LogP:	2.612
LogD:	2.351
LogS:	-4.05
# Rotatable Bonds:	7
TPSA:	126.05
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.573
Synthetic Accessibility Score:	2.751
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.772
MDCK Permeability:	2.1708836356992833e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.033
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	73.22338104248047%
Volume Distribution (VD):	0.923
Pgp-substrate:	41.05601119995117%

ADMET: Metabolism

CYP1A2-inhibitor:	0.124
CYP1A2-substrate:	0.99
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.851
CYP2C9-inhibitor:	0.475
CYP2C9-substrate:	0.828
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.611
CYP3A4-inhibitor:	0.301
CYP3A4-substrate:	0.667

ADMET: Excretion

Clearance (CL):	4.764
Half-life (T1/2):	0.636

ADMET: Toxicity

hERG Blockers:	0.376
Human Hepatotoxicity (H-HT):	0.077
Drug-inuced Liver Injury (DILI):	0.972
AMES Toxicity:	0.198
Rat Oral Acute Toxicity:	0.356
Maximum Recommended Daily Dose:	0.04
Skin Sensitization:	0.185
Carcinogencity:	0.028
Eye Corrosion:	0.003
Eye Irritation:	0.344
Respiratory Toxicity:	0.079

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

Natural Product: NPC123557

Natural Product ID:	NPC123557
*Common Name:**	LQWYACWFYYOVGS-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LQWYACWFYYOVGS-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H22O10/c1-25-11-7-9(10(22)8-12(11)26-2)16-18(27-3)14(23)13-15(24)19(28-4)21(30-6)20(29-5)17(13)31-16/h7-8,22,24H,1-6H3
SMILES:	COc1cc(c(cc1OC)O)c1c(c(=O)c2c(c(c(c(c2o1)OC)OC)OC)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44260086
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002593] 8-O-methylated flavonoids

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO11199	Agelas nakamurai	Species	Agelasidae	Eukaryota	n.a.	papua new guinean	n.a.	PMID[9784179]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7116505]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[5066072]
NPO26889	Chaetomium subaffine	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[436014]
NPO28927	Gutierrezia microcephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3655803]
NPO25583	Beta vulgaris	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33118348]
NPO24447	Thalictrum cultratum	Species	Ranunculaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29131616]
NPO8912	Daphne giraldii	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28371676]
NPO8912	Daphne giraldii	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27627130]
NPO25474	Ocotea pulchella	Species	Lauraceae	Eukaryota	n.a.	root	n.a.	PMID[27482860]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC123557 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	446
0.1-0.2	2036
0.2-0.3	5378
0.3-0.4	11430
0.4-0.5	5756
0.5-0.6	4148
0.6-0.7	5082
0.7-0.8	4838
0.8-0.85	1788
0.85-0.9	1046
0.9-0.95	573
0.95-1	176

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Similarity Score	Similarity Level	Natural Product ID
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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 NPC123557 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	412
0.1-0.2	1026
0.2-0.3	2069
0.3-0.4	2663
0.4-0.5	1627
0.5-0.6	910
0.6-0.7	297
0.7-0.8	101
0.8-0.85	24
0.85-0.9	14
0.9-0.95	6
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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