NPASS Compound

Structure

CID268829 OpenBabel06191716072D 27 31 0 0 1 0 0 0 0 0999 V2000 -0.8124 -2.4513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7161 -0.9908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5291 -0.4868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6860 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5285 -3.4061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 -1.9466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6849 0.9728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6858 -2.9199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8425 -1.4599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8425 1.4592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0139 -1.3280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3718 -1.9464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1784 0.2368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5277 -0.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5291 -1.4602 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3715 -2.9194 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6855 0.0003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8430 -1.4602 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8430 -0.4867 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9651 -1.1259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6861 -1.9469 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8425 -0.4864 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 -4.2376 -3.4194 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6877 -1.7765 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0667 -0.1588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 22 1 0 0 0 0 3 4 1 0 0 0 0 3 15 1 0 0 0 0 4 19 1 0 0 0 0 5 8 1 0 0 0 0 5 16 1 0 0 0 0 6 9 1 0 0 0 0 6 18 1 0 0 0 0 7 10 1 0 0 0 0 7 17 1 0 0 0 0 8 21 1 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 11 14 2 0 0 0 0 11 20 1 0 0 0 0 12 15 1 0 0 0 0 12 16 1 0 0 0 0 13 14 1 0 0 0 0 13 27 1 0 0 0 0 14 17 1 0 0 0 0 15 21 1 6 0 0 0 16 24 1 6 0 0 0 17 22 1 6 0 0 0 18 19 1 0 0 0 0 18 21 1 6 0 0 0 19 23 1 1 0 0 0 20 25 2 0 0 0 0 20 27 1 0 0 0 0 21 1 1 6 0 0 0 22 23 1 6 0 0 0 23 26 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	374.25
Volume:	393.47
LogP:	4.066
LogD:	3.631
LogS:	-4.399
# Rotatable Bonds:	1
TPSA:	73.83
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.672
Synthetic Accessibility Score:	4.646
Fsp3:	0.826
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:	-4.895
MDCK Permeability:	2.0455341655178927e-05
Pgp-inhibitor:	0.107
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.031
20% Bioavailability (F20%):	0.97
30% Bioavailability (F30%):	0.928

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.487
Plasma Protein Binding (PPB):	95.27046203613281%
Volume Distribution (VD):	1.346
Pgp-substrate:	4.1734466552734375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.068
CYP1A2-substrate:	0.398
CYP2C19-inhibitor:	0.036
CYP2C19-substrate:	0.53
CYP2C9-inhibitor:	0.224
CYP2C9-substrate:	0.235
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.468
CYP3A4-inhibitor:	0.67
CYP3A4-substrate:	0.196

ADMET: Excretion

Clearance (CL):	15.177
Half-life (T1/2):	0.247

ADMET: Toxicity

hERG Blockers:	0.232
Human Hepatotoxicity (H-HT):	0.453
Drug-inuced Liver Injury (DILI):	0.04
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.894
Maximum Recommended Daily Dose:	0.947
Skin Sensitization:	0.935
Carcinogencity:	0.791
Eye Corrosion:	0.009
Eye Irritation:	0.036
Respiratory Toxicity:	0.968

Download Data

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

Natural Product: NPC268829

Natural Product ID:	NPC268829
*Common Name:**	3-[(3S,5S,8R,9S,10S,13R,14S,17R)-3,14-Dihydroxy-10,13-Dimethyl-1,2,3,4,5,6,7,8,9,11,12,15,16,17-Tetradecahydrocyclopenta[A]Phenanthren-17-Yl]-2H-Furan-5-One
IUPAC Name:	3-[(3S,5S,8R,9S,10S,13R,14S,17R)-3,14-dihydroxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]-2H-furan-5-one
Synonyms:
Standard InCHIKey:	XZTUSOXSLKTKJQ-CIXPXFMPSA-N
Standard InCHI:	InChI=1S/C23H34O4/c1-21-8-5-16(24)12-15(21)3-4-19-18(21)6-9-22(2)17(7-10-23(19,22)26)14-11-20(25)27-13-14/h11,15-19,24,26H,3-10,12-13H2,1-2H3/t15-,16-,17+,18-,19+,21-,22+,23-/m0/s1
SMILES:	C[C@]12CC[C@@H](C[C@@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@H](CC[C@]12O)C1=CC(=O)OC1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL109863
PubChem CID:	92760
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001555] Cardenolides and derivatives

*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
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548837]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32649211]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31967821]
NPO33139	Pergularia tomentosa	Species	Apocynaceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[30629433]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28817274]
NPO33139	Pergularia tomentosa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19555122]
NPO9165	Asclepias curassavica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19251412]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	n.a.	root	n.a.	PMID[19052526]
NPO33139	Pergularia tomentosa	Species	Apocynaceae	Eukaryota	roots	Wadi Um Hebal, Egypt	2001-JAN	PMID[16989527]
NPO30295	Calotropis gigantea	Species	Apocynaceae	Eukaryota	leaves	n.a.	n.a.	PMID[16933890]

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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
AC50	1
EC50	1
GI50	59
IC50	9
Others	7
Potency	25

Activity Type	# Activity
Cell Line	71
Individual Protein	14
NON-MOLECULAR	2
Others	15

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT457	Cell Line	BT-549	Homo sapiens	IC50	=	3900.0	nM	PMID[454500]
NPT402	Cell Line	Hs-578T	Homo sapiens	IC50	=	3600.0	nM	PMID[454500]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	>	30000.0	nM	PMID[454500]
NPT2	Others	Unspecified		Ratio IC50	>	8.0	n.a.	PMID[454500]
NPT2	Others	Unspecified		EC50	=	2100.0	nM	PMID[454500]
NPT306	Cell Line	PC-3	Homo sapiens	IC50	=	300.0	nM	PMID[454499]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	3000.0	nM	PMID[454499]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	6000.0	nM	PMID[454499]
NPT1307	Cell Line	Calu-1	Homo sapiens	IC50	=	8000.0	nM	PMID[454499]
NPT380	Cell Line	U-251	Homo sapiens	IC50	=	6000.0	nM	PMID[454499]

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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 NPC268829 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	193
0.1-0.2	1348
0.2-0.3	4612
0.3-0.4	11318
0.4-0.5	10345
0.5-0.6	5935
0.6-0.7	5872
0.7-0.8	2714
0.8-0.85	260
0.85-0.9	76
0.9-0.95	7
0.95-1	17

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC25177
1.0	High Similarity	NPC295110
1.0	High Similarity	NPC222875
1.0	High Similarity	NPC247701
0.9789	High Similarity	NPC196471

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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 NPC268829 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	160
0.1-0.2	1470
0.2-0.3	4047
0.3-0.4	2392
0.4-0.5	583
0.5-0.6	205
0.6-0.7	185
0.7-0.8	92
0.8-0.85	12
0.85-0.9	1
0.9-0.95	3
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9167	High Similarity	NPD7638	Approved
0.9072	High Similarity	NPD7640	Approved
0.9072	High Similarity	NPD7639	Approved
0.8611	High Similarity	NPD7328	Approved
0.8611	High Similarity	NPD7327	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