NPASS Compound

Structure

NPC65615 OpenBabel07101718322D 32 36 0 0 1 0 0 0 0 0999 V2000 5.1962 -1.0000 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 1.7321 -2.0000 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 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5981 0.5000 0.0000 C 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 -0.0000 2.0000 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 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 -0.0000 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 4.3301 -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 2.5981 -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 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 2 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 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 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 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 -2.5981 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 O 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 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 -0.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 16 1 0 0 0 0 4 26 1 0 0 0 0 7 8 1 0 0 0 0 7 17 2 0 0 0 0 8 20 2 0 0 0 0 9 11 1 0 0 0 0 9 24 1 0 0 0 0 10 12 1 0 0 0 0 10 25 1 0 0 0 0 11 26 1 0 0 0 0 12 27 1 0 0 0 0 13 18 2 0 0 0 0 13 19 1 0 0 0 0 14 21 1 0 0 0 0 14 28 1 0 0 0 0 15 22 1 0 0 0 0 15 24 1 0 0 0 0 16 17 1 0 0 0 0 16 23 2 0 0 0 0 17 18 1 0 0 0 0 18 25 1 0 0 0 0 19 23 1 0 0 0 0 19 29 2 0 0 0 0 20 25 1 0 0 0 0 20 26 1 0 0 0 0 21 24 1 6 0 0 0 21 27 1 0 0 0 0 22 28 1 0 0 0 0 22 30 2 0 0 0 0 23 31 1 0 0 0 0 24 2 1 1 0 0 0 25 3 1 1 0 0 0 26 27 1 1 0 0 0 27 5 1 6 0 0 0 28 6 1 6 0 0 0 28 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	436.26
Volume:	469.404
LogP:	4.554
LogD:	3.255
LogS:	-4.185
# Rotatable Bonds:	0
TPSA:	77.76
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.54
Synthetic Accessibility Score:	5.195
Fsp3:	0.607
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.212
MDCK Permeability:	1.929868449224159e-05
Pgp-inhibitor:	0.13
Pgp-substrate:	0.022
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.583
30% Bioavailability (F30%):	0.926

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.621
Plasma Protein Binding (PPB):	96.67144775390625%
Volume Distribution (VD):	1.378
Pgp-substrate:	8.081703186035156%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.884
CYP2C19-inhibitor:	0.052
CYP2C19-substrate:	0.792
CYP2C9-inhibitor:	0.185
CYP2C9-substrate:	0.239
CYP2D6-inhibitor:	0.183
CYP2D6-substrate:	0.067
CYP3A4-inhibitor:	0.566
CYP3A4-substrate:	0.927

ADMET: Excretion

Clearance (CL):	8.456
Half-life (T1/2):	0.832

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.396
Drug-inuced Liver Injury (DILI):	0.048
AMES Toxicity:	0.202
Rat Oral Acute Toxicity:	0.208
Maximum Recommended Daily Dose:	0.721
Skin Sensitization:	0.21
Carcinogencity:	0.804
Eye Corrosion:	0.003
Eye Irritation:	0.066
Respiratory Toxicity:	0.952

Download Data

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

Natural Product: NPC65615

Natural Product ID:	NPC65615
*Common Name:**	20Beta-Hydroxytingenone
IUPAC Name:	(6aS,6bS,8aS,11R,12aR,14aR)-3,11-dihydroxy-4,6a,6b,8a,11,14a-hexamethyl-8,9,12,12a,13,14-hexahydro-7H-picene-2,10-dione
Synonyms:	20Beta-Hydroxytingenone
Standard InCHIKey:	LLINHWDEBZOLGN-CVDLMKFLSA-N
Standard InCHI:	InChI=1S/C28H36O4/c1-16-17-7-8-20-25(3,18(17)13-19(29)23(16)31)10-12-27(5)21-14-28(6,32)22(30)15-24(21,2)9-11-26(20,27)4/h7-8,13,21,31-32H,9-12,14-15H2,1-6H3/t21-,24+,25+,26-,27+,28-/m1/s1
SMILES:	CC1=C(C(=O)C=C2C1=CC=C1[C@@]2(C)CC[C@@]2(C)[C@@H]3C[C@](C)(C(=O)C[C@]3(C)CC[C@]12C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL487800
PubChem CID:	44559597
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0002088] Acyloins

*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
NPO28378	Kokoona ochracea	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8277307]
NPO28378	Kokoona ochracea	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8158155]
NPO25224	Maytenus retusa	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21090801]
NPO28378	Kokoona ochracea	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1800637]
NPO28378	Kokoona ochracea	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25224	Maytenus retusa	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28378	Kokoona ochracea	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28378	Kokoona ochracea	Species	Celastraceae	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
ED50	13
IC50	2
Others	6

Activity Type	# Activity
Cell Line	17
NON-MOLECULAR	4

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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	=	200.0	nM	PMID[465893]
NPT83	Cell Line	MCF7	Homo sapiens	Inhibition	=	100.0	%	PMID[465893]
NPT83	Cell Line	MCF7	Homo sapiens	Inhibition	=	21.0	%	PMID[465893]
NPT116	Cell Line	HL-60	Homo sapiens	Inhibition	=	90.0	%	PMID[465893]
NPT116	Cell Line	HL-60	Homo sapiens	Inhibition	=	89.0	%	PMID[465893]
NPT116	Cell Line	HL-60	Homo sapiens	Inhibition	=	80.0	%	PMID[465893]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	1400.0	nM	PMID[465893]
NPT168	Cell Line	P388	Mus musculus	ED50	=	2.0	ug ml-1	PMID[465892]
NPT453	Cell Line	HT-1080	Homo sapiens	ED50	=	2.1	ug ml-1	PMID[465892]
NPT1034	Cell Line	Lu1	Homo sapiens	ED50	=	2.2	ug ml-1	PMID[465892]

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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 NPC65615 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	1363
0.2-0.3	4982
0.3-0.4	13937
0.4-0.5	11099
0.5-0.6	6324
0.6-0.7	3861
0.7-0.8	854
0.8-0.85	47
0.85-0.9	14
0.9-0.95	8
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC68148
0.9302	High Similarity	NPC112454
0.9205	High Similarity	NPC211230
0.9101	High Similarity	NPC474328
0.9091	High Similarity	NPC174167

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 NPC65615 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	203
0.1-0.2	1638
0.2-0.3	3843
0.3-0.4	2375
0.4-0.5	704
0.5-0.6	154
0.6-0.7	167
0.7-0.8	64
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9302	High Similarity	NPD7285	Clinical (unspecified phase)
0.8471	Intermediate Similarity	NPD4695	Discontinued
0.8111	Intermediate Similarity	NPD4694	Approved
0.8111	Intermediate Similarity	NPD5280	Approved
0.8065	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