NPASS Compound

Structure

NPC258366 OpenBabel07101718312D 29 31 0 0 1 0 0 0 0 0999 V2000 -4.6046 -2.8078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9648 -1.1136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3904 1.2044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0085 -0.6977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3175 -1.6488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0303 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 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 6.0622 1.5000 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 -0.3364 1.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6581 1.4781 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 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2956 -1.8567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7213 0.4612 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7431 0.6691 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 1.7321 -1.0000 0.0000 C 0 0 0 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 5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 18 1 0 0 0 0 2 18 1 0 0 0 0 3 19 1 0 0 0 0 6 7 1 0 0 0 0 6 8 2 0 0 0 0 7 18 1 0 0 0 0 8 20 1 0 0 0 0 9 11 1 0 0 0 0 9 19 2 0 0 0 0 10 12 1 0 0 0 0 10 21 1 0 0 0 0 11 22 2 0 0 0 0 13 14 1 0 0 0 0 13 24 1 0 0 0 0 14 25 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 0 0 0 0 16 27 1 0 0 0 0 17 21 2 0 0 0 0 17 22 1 0 0 0 0 19 21 1 0 0 0 0 20 4 1 1 0 0 0 20 24 1 0 0 0 0 22 28 1 0 0 0 0 23 12 1 6 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 24 27 1 1 0 0 0 25 27 1 1 0 0 0 26 29 2 0 0 0 0 27 5 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	396.3
Volume:	454.277
LogP:	6.72
LogD:	6.191
LogS:	-5.646
# Rotatable Bonds:	7
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.51
Synthetic Accessibility Score:	4.137
Fsp3:	0.667
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.769
MDCK Permeability:	1.4348278455145191e-05
Pgp-inhibitor:	0.456
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.939
30% Bioavailability (F30%):	0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.248
Plasma Protein Binding (PPB):	98.9222183227539%
Volume Distribution (VD):	1.642
Pgp-substrate:	1.7783701419830322%

ADMET: Metabolism

CYP1A2-inhibitor:	0.203
CYP1A2-substrate:	0.688
CYP2C19-inhibitor:	0.61
CYP2C19-substrate:	0.892
CYP2C9-inhibitor:	0.531
CYP2C9-substrate:	0.975
CYP2D6-inhibitor:	0.557
CYP2D6-substrate:	0.913
CYP3A4-inhibitor:	0.832
CYP3A4-substrate:	0.392

ADMET: Excretion

Clearance (CL):	4.684
Half-life (T1/2):	0.414

ADMET: Toxicity

hERG Blockers:	0.152
Human Hepatotoxicity (H-HT):	0.519
Drug-inuced Liver Injury (DILI):	0.168
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.59
Maximum Recommended Daily Dose:	0.907
Skin Sensitization:	0.699
Carcinogencity:	0.017
Eye Corrosion:	0.031
Eye Irritation:	0.363
Respiratory Toxicity:	0.727

Download Data

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

Natural Product: NPC258366

Natural Product ID:	NPC258366
*Common Name:**	Calicoferol A
IUPAC Name:	(1R,3aS,4S,7aR)-4-[2-(5-hydroxy-2-methylphenyl)ethyl]-7a-methyl-1-[(E,2R)-6-methylhept-3-en-2-yl]-2,3,3a,4,6,7-hexahydro-1H-inden-5-one
Synonyms:
Standard InCHIKey:	MDPPOIXSNMVHOD-FBPKMIEBSA-N
Standard InCHI:	InChI=1S/C27H40O2/c1-18(2)7-6-8-20(4)24-13-14-25-23(26(29)15-16-27(24,25)5)12-10-21-17-22(28)11-9-19(21)3/h6,8-9,11,17-18,20,23-25,28H,7,10,12-16H2,1-5H3/b8-6+/t20-,23+,24-,25+,27-/m1/s1
SMILES:	CC(C)C/C=C/[C@@H](C)[C@H]1CC[C@H]2[C@H](CCc3cc(ccc3C)O)C(=O)CC[C@]12C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL518060
PubChem CID:	9547698
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO32924	gorgonian astrogorgia sp.	Species	n.a.	n.a.	n.a.	Chinese	n.a.	PMID[21982797]

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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	16
LD50	1

Activity Type	# Activity
Individual Protein	16
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1661	Individual Protein	ALK tyrosine kinase receptor	Homo sapiens	IC50	=	4160.0	nM	PMID[496786]
NPT1660	Individual Protein	NUAK family SNF1-like kinase 1	Homo sapiens	IC50	>	100000.0	nM	PMID[496786]
NPT1433	Individual Protein	Serine/threonine-protein kinase Aurora-B	Homo sapiens	IC50	>	100000.0	nM	PMID[496786]
NPT1659	Individual Protein	Tyrosine-protein kinase receptor UFO	Homo sapiens	IC50	=	14700.0	nM	PMID[496786]
NPT1436	Individual Protein	Focal adhesion kinase 1	Homo sapiens	IC50	=	9920.0	nM	PMID[496786]
NPT1438	Individual Protein	Insulin-like growth factor I receptor	Homo sapiens	IC50	=	2420.0	nM	PMID[496786]
NPT491	Individual Protein	Dual specificity mitogen-activated protein kinase kinase 1	Homo sapiens	IC50	>	100000.0	nM	PMID[496786]
NPT1337	Individual Protein	Hepatocyte growth factor receptor	Homo sapiens	IC50	=	47600.0	nM	PMID[496786]
NPT1658	Individual Protein	Serine/threonine-protein kinase NEK2	Homo sapiens	IC50	>	100000.0	nM	PMID[496786]
NPT1657	Individual Protein	Serine/threonine-protein kinase NEK6	Homo sapiens	IC50	>	100000.0	nM	PMID[496786]

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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 NPC258366 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	253
0.1-0.2	1347
0.2-0.3	2208
0.3-0.4	6478
0.4-0.5	11917
0.5-0.6	11549
0.6-0.7	7734
0.7-0.8	1127
0.8-0.85	54
0.85-0.9	20
0.9-0.95	4
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC79933
1.0	High Similarity	NPC31296
1.0	High Similarity	NPC473974
0.9561	High Similarity	NPC190501
0.9561	High Similarity	NPC318552

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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 NPC258366 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	253
0.1-0.2	892
0.2-0.3	1042
0.3-0.4	2571
0.4-0.5	2375
0.5-0.6	1532
0.6-0.7	417
0.7-0.8	55
0.8-0.85	5
0.85-0.9	6
0.9-0.95	0
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9561	High Similarity	NPD2932	Approved
0.9561	High Similarity	NPD3019	Approved
0.8824	High Similarity	NPD3023	Approved
0.8824	High Similarity	NPD3026	Approved
0.8814	High Similarity	NPD3025	Approved

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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