NPASS Compound

Structure

NPC35702 OpenBabel07101719142D 37 39 0 0 1 0 0 0 0 0999 V2000 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 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 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 -0.8660 5.5000 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 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 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 0.8660 -1.5000 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 -1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5000 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 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 -1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -2.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -2.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 O 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 1 5 2 0 0 0 0 1 13 1 0 0 0 0 2 6 2 0 0 0 0 2 14 1 0 0 0 0 3 7 2 0 0 0 0 3 13 1 0 0 0 0 4 8 2 0 0 0 0 4 14 1 0 0 0 0 5 15 1 0 0 0 0 6 16 1 0 0 0 0 7 21 1 0 0 0 0 8 22 1 0 0 0 0 9 13 2 0 0 0 0 9 17 1 0 0 0 0 10 14 2 0 0 0 0 10 18 1 0 0 0 0 11 19 1 0 0 0 0 11 25 1 0 0 0 0 12 20 1 0 0 0 0 12 25 1 0 0 0 0 15 17 2 0 0 0 0 15 26 1 0 0 0 0 16 18 2 0 0 0 0 16 27 1 0 0 0 0 17 28 1 0 0 0 0 18 29 1 0 0 0 0 19 23 1 0 0 0 0 19 30 1 1 0 0 0 20 23 1 0 0 0 0 20 36 1 6 0 0 0 21 31 2 0 0 0 0 21 36 1 0 0 0 0 22 32 2 0 0 0 0 22 37 1 0 0 0 0 23 37 1 1 0 0 0 24 25 1 0 0 0 0 24 33 2 0 0 0 0 24 34 1 0 0 0 0 25 35 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	516.13
Volume:	491.768
LogP:	1.75
LogD:	0.578
LogS:	-1.871
# Rotatable Bonds:	9
TPSA:	211.28
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.156
Synthetic Accessibility Score:	4.141
Fsp3:	0.24
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.441
MDCK Permeability:	6.999346624070313e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.658
Human Intestinal Absorption (HIA):	0.801
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.054
Plasma Protein Binding (PPB):	98.28722381591797%
Volume Distribution (VD):	0.306
Pgp-substrate:	1.6515036821365356%

ADMET: Metabolism

CYP1A2-inhibitor:	0.471
CYP1A2-substrate:	0.013
CYP2C19-inhibitor:	0.109
CYP2C19-substrate:	0.039
CYP2C9-inhibitor:	0.566
CYP2C9-substrate:	0.51
CYP2D6-inhibitor:	0.088
CYP2D6-substrate:	0.151
CYP3A4-inhibitor:	0.072
CYP3A4-substrate:	0.055

ADMET: Excretion

Clearance (CL):	3.051
Half-life (T1/2):	0.924

ADMET: Toxicity

hERG Blockers:	0.122
Human Hepatotoxicity (H-HT):	0.45
Drug-inuced Liver Injury (DILI):	0.526
AMES Toxicity:	0.062
Rat Oral Acute Toxicity:	0.125
Maximum Recommended Daily Dose:	0.092
Skin Sensitization:	0.95
Carcinogencity:	0.129
Eye Corrosion:	0.003
Eye Irritation:	0.138
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC35702

Natural Product ID:	NPC35702
*Common Name:**	UFCLZKMFXSILNL-JFZVQIRRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UFCLZKMFXSILNL-JFZVQIRRSA-N
Standard InCHI:	InChI=1S/C25H24O12/c26-15-5-1-13(9-17(15)28)3-7-21(31)36-20-12-25(35,24(33)34)11-19(30)23(20)37-22(32)8-4-14-2-6-16(27)18(29)10-14/h1-10,19-20,23,26-30,35H,11-12H2,(H,33,34)/b7-3+,8-4+/t19-,20-,23-,25-/m1/s1
SMILES:	c1cc(c(cc1/C=C/C(=O)O[C@@H]1C[C@](C[C@H]([C@H]1OC(=O)/C=C/c1ccc(c(c1)O)O)O)(C(=O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3325469
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000129] Alcohols and polyols [CHEMONTID:0001292] Cyclic alcohols and derivatives [CHEMONTID:0002509] Cyclitols and derivatives [CHEMONTID:0002512] Quinic acids 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO40047	Blumea aromatica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31646857]
NPO12728	Artemisia rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26696523]
NPO12728	Artemisia rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25176187]
NPO12728	Artemisia rupestris	Species	Asteraceae	Eukaryota	Whole plant	n.a.	n.a.	PMID[25127164]
NPO12728	Artemisia rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12728	Artemisia rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12728	Artemisia rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12728	Artemisia rupestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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

Activity Type	# Activity
IC50	1
Others	1

Activity Type	# Activity
Cell Line	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	15.5	%	PMID[449634]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	20170.0	nM	PMID[449633]

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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 NPC35702 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	327
0.1-0.2	1273
0.2-0.3	3194
0.3-0.4	7323
0.4-0.5	10285
0.5-0.6	5734
0.6-0.7	8324
0.7-0.8	5817
0.8-0.85	293
0.85-0.9	60
0.9-0.95	25
0.95-1	42

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC477335
1.0	High Similarity	NPC471027
1.0	High Similarity	NPC297517
1.0	High Similarity	NPC224389
1.0	High Similarity	NPC13818

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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 NPC35702 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	281
0.1-0.2	770
0.2-0.3	1688
0.3-0.4	2745
0.4-0.5	2034
0.5-0.6	1072
0.6-0.7	473
0.7-0.8	83
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9926	High Similarity	NPD6190	Approved
0.8312	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.831	Intermediate Similarity	NPD230	Phase 1
0.8276	Intermediate Similarity	NPD7266	Discontinued
0.8037	Intermediate Similarity	NPD7993	Clinical (unspecified phase)

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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