NPASS Compound

Structure

CID196753 OpenBabel06191715582D 32 36 0 0 1 0 0 0 0 0999 V2000 -4.4649 -0.4533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9850 1.0788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5008 -1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -0.9730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 -1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6852 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6852 -2.9189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 -2.4324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2131 1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 1.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 1.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8426 1.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3705 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0143 -0.6168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6852 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 0.4865 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6852 -0.9730 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.9730 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5279 -2.4324 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2131 0.4865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5279 1.4595 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8426 -1.4595 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5279 -1.4595 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8426 0.4865 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9873 -0.6168 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3705 -2.9189 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 25 1 0 0 0 0 6 29 1 0 0 0 0 8 9 1 0 0 0 0 8 20 2 0 0 0 0 9 23 1 0 0 0 0 10 13 1 0 0 0 0 10 22 1 0 0 0 0 11 12 1 0 0 0 0 11 24 1 0 0 0 0 12 27 1 0 0 0 0 13 30 1 0 0 0 0 14 15 1 0 0 0 0 14 25 1 0 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 16 26 1 0 0 0 0 17 29 1 0 0 0 0 18 21 1 0 0 0 0 18 25 1 0 0 0 0 19 28 1 0 0 0 0 19 31 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 0 0 0 0 21 26 1 6 0 0 0 22 27 1 1 0 0 0 22 28 1 0 0 0 0 23 27 1 1 0 0 0 23 30 1 0 0 0 0 24 28 1 1 0 0 0 24 32 1 0 0 0 0 26 3 1 1 0 0 0 27 4 1 1 0 0 0 28 5 1 6 0 0 0 29 30 1 1 0 0 0 30 7 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	442.38
Volume:	499.598
LogP:	6.539
LogD:	4.931
LogS:	-5.797
# Rotatable Bonds:	1
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.424
Synthetic Accessibility Score:	4.722
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.108
MDCK Permeability:	9.394561857334338e-06
Pgp-inhibitor:	0.015
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.652
30% Bioavailability (F30%):	0.896

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.09
Plasma Protein Binding (PPB):	96.47579193115234%
Volume Distribution (VD):	1.174
Pgp-substrate:	2.2590208053588867%

ADMET: Metabolism

CYP1A2-inhibitor:	0.028
CYP1A2-substrate:	0.272
CYP2C19-inhibitor:	0.047
CYP2C19-substrate:	0.942
CYP2C9-inhibitor:	0.14
CYP2C9-substrate:	0.212
CYP2D6-inhibitor:	0.064
CYP2D6-substrate:	0.407
CYP3A4-inhibitor:	0.627
CYP3A4-substrate:	0.497

ADMET: Excretion

Clearance (CL):	6.045
Half-life (T1/2):	0.114

ADMET: Toxicity

hERG Blockers:	0.175
Human Hepatotoxicity (H-HT):	0.213
Drug-inuced Liver Injury (DILI):	0.014
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.108
Maximum Recommended Daily Dose:	0.893
Skin Sensitization:	0.7
Carcinogencity:	0.041
Eye Corrosion:	0.028
Eye Irritation:	0.057
Respiratory Toxicity:	0.97

Download Data

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

Natural Product: NPC196753

Natural Product ID:	NPC196753
*Common Name:**	Olean-12-En-3Beta,24-Diol
IUPAC Name:	(3S,4S,4aR,6aR,6bS,8aR,12aR,14aR,14bR)-4-(hydroxymethyl)-4,6a,6b,8a,11,11,14b-heptamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-ol
Synonyms:
Standard InCHIKey:	NTWLPZMPTFQYQI-FLZFTVBESA-N
Standard InCHI:	InChI=1S/C30H50O2/c1-25(2)14-15-26(3)16-17-29(6)20(21(26)18-25)8-9-23-27(4)12-11-24(32)28(5,19-31)22(27)10-13-30(23,29)7/h8,21-24,31-32H,9-19H2,1-7H3/t21-,22+,23+,24-,26+,27-,28+,29+,30+/m0/s1
SMILES:	OC[C@@]1(C)[C@@H](O)CC[C@]2([C@H]1CC[C@@]1([C@@H]2CC=C2[C@@]1(C)CC[C@@]1([C@H]2CC(CC1)(C)C)C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL489551
PubChem CID:	14167253
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO1086	Botrytis cinerea	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32705864]
NPO8257	Carpha glomerata	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30219526]
NPO2765	Oxytropis falcata	Species	Fabaceae	Eukaryota	whole plant	Guide County, Qinghai Province, China	2008-AUG	PMID[22775441]
NPO5608	Croton gratissimus	Species	Euphorbiaceae	Eukaryota	n.a.	stem	n.a.	PMID[22032651]
NPO5608	Croton gratissimus	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22032651]
NPO2765	Oxytropis falcata	Species	Fabaceae	Eukaryota	n.a.	Sunan County, Gansu Province, China	2006-JUN	PMID[20684529]
NPO5325	Lobophytum durum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19433363]
NPO5325	Lobophytum durum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19177635]
NPO8025	Aaptos ciliata	Species	Suberitidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18257536]
NPO1086	Botrytis cinerea	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643065]

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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	2
Others	5

Activity Type	# Activity
Individual Protein	7

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT570	Individual Protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	=	30600.0	nM	PMID[553328]
NPT570	Individual Protein	Arachidonate 5-lipoxygenase	Homo sapiens	Activity	=	29.8	%	PMID[553328]
NPT1139	Individual Protein	Arachidonate 15-lipoxygenase, type II	Homo sapiens	Activity	=	100.0	%	PMID[553328]
NPT324	Individual Protein	Cyclooxygenase-1	Ovis aries	Activity	=	60.2	%	PMID[553328]
NPT31	Individual Protein	Cyclooxygenase-2	Homo sapiens	Activity	=	100.0	%	PMID[553328]
NPT1044	Individual Protein	DNA topoisomerase II alpha	Homo sapiens	IC50	>	200000.0	nM	PMID[553327]
NPT1044	Individual Protein	DNA topoisomerase II alpha	Homo sapiens	Inhibition	=	33.0	%	PMID[553327]

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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 NPC196753 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	206
0.1-0.2	1753
0.2-0.3	7209
0.3-0.4	16581
0.4-0.5	6968
0.5-0.6	4771
0.6-0.7	3565
0.7-0.8	1237
0.8-0.85	253
0.85-0.9	114
0.9-0.95	11
0.95-1	29

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC230295
1.0	High Similarity	NPC98386
1.0	High Similarity	NPC253807
1.0	High Similarity	NPC158662
0.9863	High Similarity	NPC53744

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 NPC196753 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	192
0.1-0.2	2041
0.2-0.3	4199
0.3-0.4	1947
0.4-0.5	404
0.5-0.6	174
0.6-0.7	177
0.7-0.8	13
0.8-0.85	2
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
0.9863	High Similarity	NPD7645	Phase 2
0.8481	Intermediate Similarity	NPD7525	Registered
0.8312	Intermediate Similarity	NPD6942	Approved
0.8312	Intermediate Similarity	NPD7339	Approved
0.8256	Intermediate Similarity	NPD7515	Phase 2

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