NPASS Compound

Structure

CID142563 OpenBabel06191715502D 27 30 0 0 1 0 0 0 0 0999 V2000 -1.7321 0.0000 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 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 -1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -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 -0.8660 1.5000 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 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 1 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 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 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 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 1 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 0.8660 0.5000 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 -0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 4 22 1 0 0 0 0 5 22 1 0 0 0 0 6 7 1 0 0 0 0 7 13 1 0 0 0 0 8 9 2 0 0 0 0 8 14 1 0 0 0 0 9 22 1 0 0 0 0 10 13 2 0 0 0 0 10 15 1 0 0 0 0 11 2 1 1 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 3 1 6 0 0 0 12 25 1 0 0 0 0 13 16 1 0 0 0 0 14 19 2 0 0 0 0 14 20 1 0 0 0 0 15 23 2 0 0 0 0 15 26 1 0 0 0 0 16 20 2 0 0 0 0 16 21 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 17 21 2 0 0 0 0 18 24 1 1 0 0 0 19 25 1 0 0 0 0 20 27 1 0 0 0 0 21 26 1 0 0 0 0 22 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	370.18
Volume:	382.975
LogP:	5.59
LogD:	4.38
LogS:	-3.452
# Rotatable Bonds:	2
TPSA:	68.9
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.795
Synthetic Accessibility Score:	4.171
Fsp3:	0.5
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:	-4.737
MDCK Permeability:	1.7453281543566845e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.02
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.109

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.092
Plasma Protein Binding (PPB):	91.8418197631836%
Volume Distribution (VD):	1.503
Pgp-substrate:	7.058825969696045%

ADMET: Metabolism

CYP1A2-inhibitor:	0.537
CYP1A2-substrate:	0.843
CYP2C19-inhibitor:	0.478
CYP2C19-substrate:	0.804
CYP2C9-inhibitor:	0.675
CYP2C9-substrate:	0.812
CYP2D6-inhibitor:	0.806
CYP2D6-substrate:	0.299
CYP3A4-inhibitor:	0.554
CYP3A4-substrate:	0.298

ADMET: Excretion

Clearance (CL):	5.358
Half-life (T1/2):	0.197

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.886
Drug-inuced Liver Injury (DILI):	0.893
AMES Toxicity:	0.061
Rat Oral Acute Toxicity:	0.956
Maximum Recommended Daily Dose:	0.819
Skin Sensitization:	0.269
Carcinogencity:	0.893
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.673

Download Data

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

Natural Product: NPC142563

Natural Product ID:	NPC142563
*Common Name:**	Costatolide
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NIDRYBLTWYFCFV-PZROIBLQSA-N
Standard InCHI:	InChI=1S/C22H26O5/c1-6-7-13-10-15(23)26-21-16(13)20-14(8-9-22(4,5)27-20)19-17(21)18(24)11(2)12(3)25-19/h8-12,18,24H,6-7H2,1-5H3/t11-,12-,18-/m0/s1
SMILES:	CCCc1cc(=O)oc2c1c1OC(C)(C)C=Cc1c1c2[C@@H](O)[C@H]([C@@H](O1)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL7187
PubChem CID:	461128
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0003484] Pyranocoumarins [CHEMONTID:0003485] Angular pyranocoumarins

*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
NPO19800.1	Calophyllum teysmannii var. inophylloide	Varieties	Calophyllaceae	Eukaryota	n.a.	latex	n.a.	PMID[9784162]
NPO19800	Calophyllum teysmannii	Species	Calophyllaceae	Eukaryota	n.a.	latex	n.a.	PMID[8864237]
NPO19800.1	Calophyllum teysmannii var. inophylloide	Varieties	Calophyllaceae	Eukaryota	n.a.	stem	n.a.	PMID[8792623]
NPO19800	Calophyllum teysmannii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8792623]
NPO17406	Calophyllum lanigerum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8792623]
NPO25528	Calophyllum brasiliense	Species	Calophyllaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15340243]
NPO25528	Calophyllum brasiliense	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104480]
NPO17406	Calophyllum lanigerum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1379639]
NPO25528	Calophyllum brasiliense	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12662094]
NPO25528	Calophyllum brasiliense	Species	Calophyllaceae	Eukaryota	n.a.	stem	n.a.	PMID[11908963]

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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
EC50	4
IC50	12
Others	15

Activity Type	# Activity
Cell Line	12
Individual Protein	9
NON-MOLECULAR	1
Organism	4
Others	2
Uncleic Acid	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	IC50	=	1400.0	nM	PMID[526758]
NPT459	Individual Protein	Human immunodeficiency virus type 1 reverse transcriptase	Human immunodeficiency virus 1	IC50	=	290.0	nM	PMID[526758]
NPT759	Cell Line	H9	Homo sapiens	IC50	=	9800.0	nM	PMID[526757]
NPT27	Others	Unspecified		Ratio IC50/EC50	=	44.5	n.a.	PMID[526757]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	220.0	nM	PMID[526757]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	200.0	nM	PMID[526756]
NPT27	Others	Unspecified		TI	>	20.0	n.a.	PMID[526756]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	300.0	nM	PMID[526755]
NPT315	Cell Line	CEM-SS	Homo sapiens	EC50	=	200.0	nM	PMID[526754]
NPT315	Cell Line	CEM-SS	Homo sapiens	IC50	=	5900.0	nM	PMID[526754]

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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 NPC142563 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	349
0.1-0.2	1453
0.2-0.3	3303
0.3-0.4	7663
0.4-0.5	11153
0.5-0.6	4091
0.6-0.7	6010
0.7-0.8	5344
0.8-0.85	2090
0.85-0.9	965
0.9-0.95	249
0.95-1	27

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC205797
1.0	High Similarity	NPC241165
1.0	High Similarity	NPC1220
1.0	High Similarity	NPC291551
1.0	High Similarity	NPC141822

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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 NPC142563 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	311
0.1-0.2	930
0.2-0.3	1603
0.3-0.4	2518
0.4-0.5	2044
0.5-0.6	1127
0.6-0.7	414
0.7-0.8	149
0.8-0.85	37
0.85-0.9	13
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD5123	Clinical (unspecified phase)
1.0	High Similarity	NPD5124	Phase 1
0.8462	Intermediate Similarity	NPD422	Phase 1
0.8309	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.8239	Intermediate Similarity	NPD1652	Phase 2

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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