NPASS Compound

Structure

CID206079 OpenBabel06191715592D 29 31 0 0 1 0 0 0 0 0999 V2000 -1.6953 2.1395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6275 2.7681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4500 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6797 1.5431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2748 1.4466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2785 1.6275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5601 1.0712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7446 -1.2825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9295 0.4869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4181 -1.4228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0702 0.5813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7427 -0.1115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2529 1.0712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6238 2.5872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8670 -0.2240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7427 0.5813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3597 -0.2860 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9653 3.3661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1307 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9642 0.8162 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2529 -0.6013 0.0000 C 0 0 2 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 0.6231 -0.7564 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8110 1.0238 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3105 4.3258 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9615 3.1852 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9986 1.0992 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5279 0.2534 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1442 1.1943 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 14 1 0 0 0 0 3 15 1 0 0 0 0 5 6 1 0 0 0 0 5 9 2 0 0 0 0 6 14 2 0 0 0 0 7 11 1 0 0 0 0 7 13 2 0 0 0 0 8 10 1 0 0 0 0 8 17 1 0 0 0 0 9 20 1 0 0 0 0 10 21 1 0 0 0 0 11 22 1 0 0 0 0 12 16 1 0 0 0 0 12 21 1 0 0 0 0 13 16 1 0 0 0 0 14 18 1 0 0 0 0 15 23 2 0 0 0 0 15 28 1 0 0 0 0 16 24 2 0 0 0 0 17 20 1 6 0 0 0 17 22 1 0 0 0 0 18 25 2 0 0 0 0 18 26 1 0 0 0 0 19 21 1 0 0 0 0 19 27 2 0 0 0 0 19 29 1 0 0 0 0 20 4 1 1 0 0 0 20 29 1 0 0 0 0 21 22 1 1 0 0 0 22 28 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	402.17
Volume:	406.475
LogP:	1.371
LogD:	0.093
LogS:	-3.413
# Rotatable Bonds:	5
TPSA:	106.97
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.333
Synthetic Accessibility Score:	5.747
Fsp3:	0.545
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:	-5.303
MDCK Permeability:	1.531342786620371e-05
Pgp-inhibitor:	0.01
Pgp-substrate:	0.578
Human Intestinal Absorption (HIA):	0.087
20% Bioavailability (F20%):	0.018
30% Bioavailability (F30%):	0.49

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.689
Plasma Protein Binding (PPB):	65.91092681884766%
Volume Distribution (VD):	0.206
Pgp-substrate:	29.272764205932617%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.713
CYP2C19-inhibitor:	0.043
CYP2C19-substrate:	0.097
CYP2C9-inhibitor:	0.036
CYP2C9-substrate:	0.297
CYP2D6-inhibitor:	0.028
CYP2D6-substrate:	0.122
CYP3A4-inhibitor:	0.436
CYP3A4-substrate:	0.252

ADMET: Excretion

Clearance (CL):	1.873
Half-life (T1/2):	0.714

ADMET: Toxicity

hERG Blockers:	0.02
Human Hepatotoxicity (H-HT):	0.153
Drug-inuced Liver Injury (DILI):	0.81
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.748
Maximum Recommended Daily Dose:	0.032
Skin Sensitization:	0.069
Carcinogencity:	0.908
Eye Corrosion:	0.005
Eye Irritation:	0.017
Respiratory Toxicity:	0.562

Download Data

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

Natural Product: NPC206079

Natural Product ID:	NPC206079
*Common Name:**	Pseudolaric Acid F
IUPAC Name:	n.a.
Synonyms:	Pseudolaric Acid F
Standard InCHIKey:	UBHOILGODYTXTA-MRFLEFCVSA-N
Standard InCHI:	InChI=1S/C22H26O7/c1-13-7-11-22(28-15(3)23)17-8-10-21(22,12-16(13)24)19(27)29-20(17,4)9-5-6-14(2)18(25)26/h5-7,9,17H,8,10-12H2,1-4H3,(H,25,26)/b9-5+,14-6+/t17-,20+,21-,22-/m0/s1
SMILES:	CC1=CC[C@@]2([C@H]3CC[C@]2(CC1=O)C(=O)O[C@]3(C)/C=C/C=C(C)/C(=O)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL374201
PubChem CID:	636647
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO29968	Pseudolarix kaempferi	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8377017]
NPO16955	Pseudolarix amabilis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7760078]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25843525]
NPO385	Bipolaris oryzae	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23668986]
NPO29968	Pseudolarix kaempferi	Species	Pinaceae	Eukaryota	root and trunk bark	n.a.	n.a.	PMID[18078313]
NPO29968	Pseudolarix kaempferi	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18078313]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17381154]
NPO29968	Pseudolarix kaempferi	Species	Pinaceae	Eukaryota	bark	n.a.	n.a.	PMID[17291040]
NPO16955	Pseudolarix amabilis	Species	Pinaceae	Eukaryota	leaves,?stems	USA	n.a.	PMID[16124770]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	tuber	n.a.	PMID[15180301]

Showing 1 to 10 of 36 entries

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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	5

Activity Type	# Activity
Cell Line	2
NON-MOLECULAR	1
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[520141]
NPT27	Others	Unspecified	""	IC50	>	10000.0	nM	PMID[520141]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[520141]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	55440.0	nM	PMID[520140]
NPT27	Others	Unspecified	""	IC50	>	100000.0	nM	PMID[520140]

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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 NPC206079 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	195
0.1-0.2	1056
0.2-0.3	4164
0.3-0.4	9112
0.4-0.5	14578
0.5-0.6	7633
0.6-0.7	4997
0.7-0.8	941
0.8-0.85	9
0.85-0.9	4
0.9-0.95	5
0.95-1	3

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Similarity Score	Similarity Level	Natural Product ID
0.9574	High Similarity	NPC64742
0.957	High Similarity	NPC9812
0.9368	High Similarity	NPC244411
0.9286	High Similarity	NPC309190
0.9175	High Similarity	NPC62670

Showing 1 to 5 of 200 entries

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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 NPC206079 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	169
0.1-0.2	1315
0.2-0.3	3532
0.3-0.4	2723
0.4-0.5	909
0.5-0.6	273
0.6-0.7	209
0.7-0.8	20
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7879	Intermediate Similarity	NPD5785	Approved
0.7745	Intermediate Similarity	NPD1698	Clinical (unspecified phase)
0.7477	Intermediate Similarity	NPD6371	Approved
0.7475	Intermediate Similarity	NPD5786	Approved
0.7374	Intermediate Similarity	NPD5363	Approved

Showing 1 to 5 of 200 entries

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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