NPASS Compound

Structure

CID250046 OpenBabel06191716052D 41 44 0 0 1 0 0 0 0 0999 V2000 0.4177 -3.1730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 3.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7899 -1.8827 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 0.1589 -2.2071 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 5.1962 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 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 -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 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 5.0000 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 1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 1 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 1.7321 3.0000 0.0000 C 0 0 1 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 0.8660 3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 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 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 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 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 5.0000 0.0000 O 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 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 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 -0.8660 -1.5000 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 2.5981 3.5000 0.0000 O 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 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 8 2 0 0 0 0 2 16 1 0 0 0 0 3 17 1 0 0 0 0 4 28 1 0 0 0 0 5 28 1 0 0 0 0 8 29 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 10 12 1 0 0 0 0 11 13 2 0 0 0 0 12 18 2 0 0 0 0 13 18 1 0 0 0 0 14 20 1 0 0 0 0 14 21 1 0 0 0 0 15 19 1 0 0 0 0 15 29 1 0 0 0 0 16 32 2 0 0 0 0 16 39 1 0 0 0 0 17 33 2 0 0 0 0 17 40 1 0 0 0 0 18 26 1 0 0 0 0 19 23 1 0 0 0 0 19 34 1 6 0 0 0 20 28 1 0 0 0 0 20 30 1 1 0 0 0 21 31 1 6 0 0 0 21 35 1 0 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 22 39 1 6 0 0 0 23 30 1 1 0 0 0 23 31 1 0 0 0 0 24 28 1 0 0 0 0 24 40 1 6 0 0 0 25 30 1 6 0 0 0 25 41 1 0 0 0 0 26 36 2 0 0 0 0 26 41 1 0 0 0 0 27 29 1 0 0 0 0 27 31 1 0 0 0 0 27 37 2 0 0 0 0 29 6 1 1 0 0 0 30 7 1 1 0 0 0 31 38 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	572.26
Volume:	577.317
LogP:	3.168
LogD:	2.004
LogS:	-4.312
# Rotatable Bonds:	8
TPSA:	156.66
# H-Bond Aceptor:	10
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.272
Synthetic Accessibility Score:	5.14
Fsp3:	0.613
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.197
MDCK Permeability:	3.894876499543898e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.916
Human Intestinal Absorption (HIA):	0.613
20% Bioavailability (F20%):	0.621
30% Bioavailability (F30%):	0.81

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.678
Plasma Protein Binding (PPB):	76.8551025390625%
Volume Distribution (VD):	1.131
Pgp-substrate:	29.453018188476562%

ADMET: Metabolism

CYP1A2-inhibitor:	0.021
CYP1A2-substrate:	0.065
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.206
CYP2C9-inhibitor:	0.034
CYP2C9-substrate:	0.103
CYP2D6-inhibitor:	0.254
CYP2D6-substrate:	0.093
CYP3A4-inhibitor:	0.802
CYP3A4-substrate:	0.339

ADMET: Excretion

Clearance (CL):	2.339
Half-life (T1/2):	0.772

ADMET: Toxicity

hERG Blockers:	0.216
Human Hepatotoxicity (H-HT):	0.251
Drug-inuced Liver Injury (DILI):	0.627
AMES Toxicity:	0.262
Rat Oral Acute Toxicity:	0.859
Maximum Recommended Daily Dose:	0.81
Skin Sensitization:	0.211
Carcinogencity:	0.05
Eye Corrosion:	0.005
Eye Irritation:	0.018
Respiratory Toxicity:	0.958

Download Data

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

Natural Product: NPC250046

Natural Product ID:	NPC250046
*Common Name:**	Orthosiphol G
IUPAC Name:	[(2S,3S,4R,4aS,4bS,5R,7R,8aR,9R,10aS)-2,3-diacetyloxy-7-ethenyl-5,8a,9-trihydroxy-1,1,4a,7-tetramethyl-8-oxo-3,4,4b,5,6,9,10,10a-octahydro-2H-phenanthren-4-yl] benzoate
Synonyms:	Orthosiphol G
Standard InCHIKey:	HVCLVVFTATWQBZ-SRHIYTGZSA-N
Standard InCHI:	InChI=1S/C31H40O10/c1-8-29(6)15-19(34)23-30(7)20(14-21(35)31(23,38)27(29)37)28(4,5)24(40-17(3)33)22(39-16(2)32)25(30)41-26(36)18-12-10-9-11-13-18/h8-13,19-25,34-35,38H,1,14-15H2,2-7H3/t19-,20+,21-,22+,23-,24-,25+,29+,30+,31+/m1/s1
SMILES:	C=C[C@@]1(C)C[C@@H](O)[C@H]2[C@@](C1=O)(O)[C@H](O)C[C@@H]1[C@]2(C)[C@@H](OC(=O)c2ccccc2)[C@@H](OC(=O)C)[C@H](C1(C)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL448947
PubChem CID:	10076785
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.		PMID[31861466]
NPO3549	Euonymus maackii	Species	Celastraceae	Eukaryota	Seeds	n.a.	n.a.	PMID[31713425]
NPO23000	Zephyranthes carinata	Species	Amaryllidaceae	Eukaryota	Whole Plants	n.a.	n.a.	PMID[28898076]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[26860358]
NPO19152	Empetrum nigrum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26473275]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	seed	n.a.	PMID[25433632]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24310066]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23849114]
NPO8541	Oryza sativa	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23700450]
NPO5877	Morus yunnanensis	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22165973]

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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	1

Activity Type	# Activity
CELL-LINE	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20763	CELL-LINE	J774.1	Mus musculus	IC50	=	145000.0	nM	PMID[567425]

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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 NPC250046 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	339
0.1-0.2	1136
0.2-0.3	2446
0.3-0.4	4683
0.4-0.5	8889
0.5-0.6	10441
0.6-0.7	10872
0.7-0.8	3365
0.8-0.85	263
0.85-0.9	206
0.9-0.95	26
0.95-1	31

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC60509
1.0	High Similarity	NPC81698
0.9929	High Similarity	NPC198455
0.9929	High Similarity	NPC161239
0.9929	High Similarity	NPC165260

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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 NPC250046 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	282
0.1-0.2	773
0.2-0.3	1559
0.3-0.4	2820
0.4-0.5	2233
0.5-0.6	1060
0.6-0.7	353
0.7-0.8	68
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8456	Intermediate Similarity	NPD7236	Approved
0.8301	Intermediate Similarity	NPD7239	Suspended
0.8293	Intermediate Similarity	NPD8368	Discontinued
0.8272	Intermediate Similarity	NPD7799	Discontinued
0.8166	Intermediate Similarity	NPD8435	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