NPASS Compound

Structure

CID66110 OpenBabel06191715402D 31 33 0 0 1 0 0 0 0 0999 V2000 4.6131 2.7561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4295 -0.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6660 1.5314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2378 3.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2609 1.4350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2644 1.6158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7182 0.5732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5522 1.0561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7341 -1.2644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9157 0.4755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7182 -0.1099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4122 -1.4028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0692 0.5732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6096 2.5753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8548 -0.2209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2352 1.0561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3405 -0.2820 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9512 3.3540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6714 2.1093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1148 0.5554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9506 0.8047 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2352 -0.5929 0.0000 C 0 0 1 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 0.6143 -0.7457 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2964 4.3135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9477 3.1731 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9775 3.0137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9824 1.0911 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8016 2.2581 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5205 0.2498 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1421 1.1775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 4 29 1 0 0 0 0 5 6 1 0 0 0 0 5 10 2 0 0 0 0 6 14 2 0 0 0 0 7 11 1 0 0 0 0 7 16 2 0 0 0 0 8 13 1 0 0 0 0 8 16 1 0 0 0 0 9 12 1 0 0 0 0 9 17 1 0 0 0 0 10 21 1 0 0 0 0 11 22 1 0 0 0 0 12 22 1 0 0 0 0 13 23 1 0 0 0 0 14 18 1 0 0 0 0 15 24 2 0 0 0 0 15 30 1 0 0 0 0 16 19 1 0 0 0 0 17 21 1 6 0 0 0 17 23 1 0 0 0 0 18 25 2 0 0 0 0 18 26 1 0 0 0 0 19 27 2 0 0 0 0 19 29 1 0 0 0 0 20 22 1 0 0 0 0 20 28 2 0 0 0 0 20 31 1 0 0 0 0 21 3 1 1 0 0 0 21 31 1 0 0 0 0 22 23 1 1 0 0 0 23 30 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.18
Volume:	432.561
LogP:	1.416
LogD:	0.909
LogS:	-3.615
# Rotatable Bonds:	7
TPSA:	116.2
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.305
Synthetic Accessibility Score:	5.33
Fsp3:	0.565
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:	-5.175
MDCK Permeability:	1.911618164740503e-05
Pgp-inhibitor:	0.766
Pgp-substrate:	0.022
Human Intestinal Absorption (HIA):	0.019
20% Bioavailability (F20%):	0.905
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.494
Plasma Protein Binding (PPB):	62.69595718383789%
Volume Distribution (VD):	0.238
Pgp-substrate:	21.66768455505371%

ADMET: Metabolism

CYP1A2-inhibitor:	0.027
CYP1A2-substrate:	0.711
CYP2C19-inhibitor:	0.194
CYP2C19-substrate:	0.126
CYP2C9-inhibitor:	0.177
CYP2C9-substrate:	0.571
CYP2D6-inhibitor:	0.141
CYP2D6-substrate:	0.192
CYP3A4-inhibitor:	0.473
CYP3A4-substrate:	0.305

ADMET: Excretion

Clearance (CL):	2.467
Half-life (T1/2):	0.661

ADMET: Toxicity

hERG Blockers:	0.029
Human Hepatotoxicity (H-HT):	0.455
Drug-inuced Liver Injury (DILI):	0.639
AMES Toxicity:	0.089
Rat Oral Acute Toxicity:	0.32
Maximum Recommended Daily Dose:	0.407
Skin Sensitization:	0.517
Carcinogencity:	0.744
Eye Corrosion:	0.027
Eye Irritation:	0.074
Respiratory Toxicity:	0.288

Download Data

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

Natural Product: NPC66110

Natural Product ID:	NPC66110
*Common Name:**	Pseudolaric Acid B
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VDGOFNMYZYBUDT-YDRCMHEVSA-N
Standard InCHI:	InChI=1S/C23H28O8/c1-14(18(25)26)6-5-10-21(3)17-9-12-22(20(28)31-21)11-7-16(19(27)29-4)8-13-23(17,22)30-15(2)24/h5-7,10,17H,8-9,11-13H2,1-4H3,(H,25,26)/b10-5+,14-6+/t17-,21+,22+,23-/m0/s1
SMILES:	COC(=O)C1=CC[C@@]23[C@@](CC1)(OC(=O)C)[C@@H](CC2)[C@@](OC3=O)(C)/C=C/C=C(/C(=O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL218534
PubChem CID:	6475943
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]

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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	20
LD50	2
MIC	17
Others	35

Activity Type	# Activity
Cell Line	15
CELL-LINE	2
NON-MOLECULAR	2
Organism	52
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	6.25	ug.mL-1	PMID[560309]
NPT1533	Organism	Saccharomyces	Saccharomyces	MIC	=	12.5	ug.mL-1	PMID[560309]
NPT327	Organism	Microsporum gypseum	Microsporum gypseum	MIC	=	12.5	ug.mL-1	PMID[560309]
NPT329	Organism	Trichophyton rubrum	Trichophyton rubrum	MIC	=	25.0	ug.mL-1	PMID[560309]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	4200.0	nM	PMID[560308]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	1600.0	nM	PMID[560308]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	=	1300.0	nM	PMID[560308]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	300.0	nM	PMID[560307]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	6.25	ug.mL-1	PMID[560306]
NPT327	Organism	Microsporum gypseum	Microsporum gypseum	MIC	=	12.5	ug.mL-1	PMID[560306]

Showing 1 to 10 of 65 entries

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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 NPC66110 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	189
0.1-0.2	1017
0.2-0.3	3928
0.3-0.4	8025
0.4-0.5	14472
0.5-0.6	8288
0.6-0.7	5678
0.7-0.8	1078
0.8-0.85	9
0.85-0.9	1
0.9-0.95	5
0.95-1	7

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Similarity Score	Similarity Level	Natural Product ID
0.9894	High Similarity	NPC62670
0.9894	High Similarity	NPC116139
0.9681	High Similarity	NPC244411
0.9574	High Similarity	NPC47834
0.9468	High Similarity	NPC9812

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 NPC66110 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	156
0.1-0.2	1308
0.2-0.3	3582
0.3-0.4	2663
0.4-0.5	926
0.5-0.6	281
0.6-0.7	221
0.7-0.8	13
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
0.7568	Intermediate Similarity	NPD6371	Approved
0.7451	Intermediate Similarity	NPD5785	Approved
0.7333	Intermediate Similarity	NPD1698	Clinical (unspecified phase)
0.7308	Intermediate Similarity	NPD5779	Approved
0.7308	Intermediate Similarity	NPD5778	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