NPASS Compound

Structure

CID100586 OpenBabel06191715442D 34 38 0 0 1 0 0 0 0 0999 V2000 -6.1767 0.9294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5082 0.0652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2388 0.9094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2389 1.8694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0291 1.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8607 -1.4236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.9603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1969 0.0201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5846 -1.0354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4064 -1.3893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6044 2.7790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4489 -0.7040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8654 -0.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8022 2.3161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6044 -1.8523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8020 1.3897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8025 -0.4633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4069 -0.4636 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6044 0.9263 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6049 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.9266 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4069 2.3156 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6045 -0.0003 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6050 0.9267 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5940 0.2102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4072 1.3895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8025 1.3900 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8025 -0.4633 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 -4.0105 0.4615 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4275 1.4015 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4280 -0.4752 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2299 2.7910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8748 0.7930 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 3 26 1 0 0 0 0 4 26 1 0 0 0 0 6 28 1 0 0 0 0 9 12 1 0 0 0 0 9 13 1 0 0 0 0 10 15 1 0 0 0 0 11 14 1 0 0 0 0 11 22 1 0 0 0 0 12 25 1 0 0 0 0 13 30 1 0 0 0 0 14 27 1 0 0 0 0 15 28 1 0 0 0 0 16 19 1 0 0 0 0 16 21 1 0 0 0 0 17 20 1 0 0 0 0 17 29 1 0 0 0 0 18 10 1 6 0 0 0 18 23 1 0 0 0 0 18 30 1 0 0 0 0 19 23 1 0 0 0 0 19 31 1 6 0 0 0 20 24 1 0 0 0 0 20 32 1 1 0 0 0 21 27 1 6 0 0 0 21 29 1 0 0 0 0 22 26 1 0 0 0 0 22 33 1 6 0 0 0 23 28 1 1 0 0 0 24 26 1 0 0 0 0 24 27 1 6 0 0 0 25 34 1 0 0 0 0 27 5 1 6 0 0 0 28 29 1 6 0 0 0 29 7 1 6 0 0 0 30 8 1 1 0 0 0 30 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	476.39
Volume:	519.815
LogP:	5.099
LogD:	4.93
LogS:	-4.648
# Rotatable Bonds:	1
TPSA:	69.92
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.453
Synthetic Accessibility Score:	5.063
Fsp3:	1.0
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:	-4.892
MDCK Permeability:	3.85949679184705e-05
Pgp-inhibitor:	0.984
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.017
30% Bioavailability (F30%):	0.24

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.057
Plasma Protein Binding (PPB):	91.16184997558594%
Volume Distribution (VD):	0.836
Pgp-substrate:	5.401648044586182%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.329
CYP2C19-inhibitor:	0.042
CYP2C19-substrate:	0.927
CYP2C9-inhibitor:	0.159
CYP2C9-substrate:	0.354
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.464
CYP3A4-inhibitor:	0.518
CYP3A4-substrate:	0.318

ADMET: Excretion

Clearance (CL):	6.039
Half-life (T1/2):	0.2

ADMET: Toxicity

hERG Blockers:	0.125
Human Hepatotoxicity (H-HT):	0.365
Drug-inuced Liver Injury (DILI):	0.019
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.399
Maximum Recommended Daily Dose:	0.36
Skin Sensitization:	0.456
Carcinogencity:	0.012
Eye Corrosion:	0.532
Eye Irritation:	0.061
Respiratory Toxicity:	0.979

Download Data

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

Natural Product: NPC100586

Natural Product ID:	NPC100586
*Common Name:**	(3S,5R,6S,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-Pentamethyl-17-[(2S)-2,6,6-Trimethyloxan-2-Yl]-2,3,5,6,7,9,11,12,13,15,16,17-Dodecahydro-1H-Cyclopenta[A]Phenanthrene-3,6,12-Triol
IUPAC Name:	(3S,5R,6S,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-pentamethyl-17-[(2S)-2,6,6-trimethyloxan-2-yl]-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,6,12-triol
Synonyms:
Standard InCHIKey:	QFJUYMMIBFBOJY-AQIAMZLMSA-N
Standard InCHI:	InChI=1S/C30H52O4/c1-25(2)12-9-13-30(8,34-25)18-10-15-28(6)23(18)19(31)16-21-27(5)14-11-22(33)26(3,4)24(27)20(32)17-29(21,28)7/h18-24,31-33H,9-17H2,1-8H3/t18-,19+,20-,21+,22-,23-,24-,27+,28+,29+,30-/m0/s1
SMILES:	O[C@H]1C[C@]2(C)[C@@H]([C@@]3([C@@H]1C(C)(C)[C@@H](O)CC3)C)C[C@H]([C@H]1[C@@]2(C)CC[C@@H]1[C@]1(C)CCCC(O1)(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1357750
PubChem CID:	12313936
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129622]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[28345906]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[27914541]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	stems-leaves	n.a.	n.a.	PMID[26420067]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Steamed Roots	n.a.	n.a.	PMID[26200131]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25152999]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24968750]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24290061]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	berry	n.a.	n.a.	PMID[21216145]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[2092947]

Showing 1 to 10 of 27 entries

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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
Potency	7

Activity Type	# Activity
Individual Protein	4
Others	2
Protein-Protein Interaction	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT442	Individual Protein	Ferritin light chain	Equus caballus	Potency	=	35481.3	nM	PMID[538237]
NPT531	Individual Protein	Nuclear receptor ROR-gamma	Mus musculus	Potency	=	44.7	nM	PMID[538237]
NPT531	Individual Protein	Nuclear receptor ROR-gamma	Mus musculus	Potency	=	199.5	nM	PMID[538236]
NPT2	Others	Unspecified		Potency	=	31622.8	nM	PMID[538236]
NPT791	Individual Protein	Cruzipain	Trypanosoma cruzi	Potency	=	39810.7	nM	PMID[538236]
NPT197	Protein-Protein Interaction	Menin/Histone-lysine N-methyltransferase MLL	Homo sapiens	Potency	=	2818.4	nM	PMID[538236]
NPT2	Others	Unspecified		Potency	n.a.	6309.6	nM	PMID[538236]

Showing 1 to 7 of 7 entries

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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 NPC100586 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	396
0.1-0.2	4232
0.2-0.3	15914
0.3-0.4	9656
0.4-0.5	4645
0.5-0.6	4233
0.6-0.7	2646
0.7-0.8	794
0.8-0.85	134
0.85-0.9	31
0.9-0.95	11
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC157422
1.0	High Similarity	NPC109457
0.9848	High Similarity	NPC282454
0.9412	High Similarity	NPC473279
0.9254	High Similarity	NPC472741

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 NPC100586 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	393
0.1-0.2	4197
0.2-0.3	3261
0.3-0.4	753
0.4-0.5	220
0.5-0.6	221
0.6-0.7	76
0.7-0.8	26
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8841	High Similarity	NPD4267	Clinical (unspecified phase)
0.8194	Intermediate Similarity	NPD4787	Phase 1
0.8182	Intermediate Similarity	NPD6928	Phase 2
0.8026	Intermediate Similarity	NPD6116	Phase 1
0.7949	Intermediate Similarity	NPD7525	Registered

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