NPASS Compound

Structure

CID107039 OpenBabel06191715452D 32 35 0 0 1 0 0 0 0 0999 V2000 -3.3679 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5259 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0518 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3679 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3281 -2.3003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2098 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6839 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 -3.1423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3679 1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3559 -2.3003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 0.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5259 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2098 0.4861 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3679 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6839 -0.9722 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6839 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9722 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3559 -3.9842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 0.4861 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5259 1.4583 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8420 -1.4583 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8420 0.4861 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 -0.8420 -4.8262 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6164 -3.9842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 19 2 0 0 0 0 2 19 1 0 0 0 0 7 29 1 0 0 0 0 9 10 1 0 0 0 0 9 23 2 0 0 0 0 10 24 1 0 0 0 0 11 14 1 0 0 0 0 11 20 1 0 0 0 0 12 16 1 0 0 0 0 12 22 1 0 0 0 0 13 15 1 0 0 0 0 13 25 1 0 0 0 0 14 27 1 0 0 0 0 15 28 1 0 0 0 0 16 30 1 0 0 0 0 17 18 1 0 0 0 0 17 27 1 0 0 0 0 18 29 1 0 0 0 0 19 22 1 0 0 0 0 20 3 1 1 0 0 0 20 21 1 0 0 0 0 21 4 1 6 0 0 0 21 26 1 0 0 0 0 22 28 1 6 0 0 0 23 26 1 0 0 0 0 23 29 1 0 0 0 0 24 28 1 6 0 0 0 24 30 1 0 0 0 0 25 31 2 0 0 0 0 25 32 1 0 0 0 0 26 27 1 1 0 0 0 27 5 1 6 0 0 0 28 6 1 6 0 0 0 29 30 1 6 0 0 0 30 8 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	402.35
Volume:	456.266
LogP:	6.328
LogD:	5.597
LogS:	-5.537
# Rotatable Bonds:	5
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.525
Synthetic Accessibility Score:	4.376
Fsp3:	0.926
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:	-4.631
MDCK Permeability:	1.587585029483307e-05
Pgp-inhibitor:	0.954
Pgp-substrate:	0.986
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.992
30% Bioavailability (F30%):	0.064

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.261
Plasma Protein Binding (PPB):	94.04622650146484%
Volume Distribution (VD):	1.211
Pgp-substrate:	1.2503753900527954%

ADMET: Metabolism

CYP1A2-inhibitor:	0.108
CYP1A2-substrate:	0.488
CYP2C19-inhibitor:	0.068
CYP2C19-substrate:	0.87
CYP2C9-inhibitor:	0.206
CYP2C9-substrate:	0.137
CYP2D6-inhibitor:	0.024
CYP2D6-substrate:	0.633
CYP3A4-inhibitor:	0.324
CYP3A4-substrate:	0.598

ADMET: Excretion

Clearance (CL):	9.84
Half-life (T1/2):	0.074

ADMET: Toxicity

hERG Blockers:	0.358
Human Hepatotoxicity (H-HT):	0.259
Drug-inuced Liver Injury (DILI):	0.291
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.006
Maximum Recommended Daily Dose:	0.509
Skin Sensitization:	0.949
Carcinogencity:	0.263
Eye Corrosion:	0.385
Eye Irritation:	0.442
Respiratory Toxicity:	0.911

Download Data

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

Natural Product: NPC107039

Natural Product ID:	NPC107039
*Common Name:**	Roburic Acid
IUPAC Name:	3-[(1S,2S,4aR,4bS,6aR,9R,10S,10aR,12aR)-1,4a,4b,6a,9,10-hexamethyl-2-prop-1-en-2-yl-2,3,4,5,6,7,8,9,10,10a,12,12a-dodecahydrochrysen-1-yl]propanoic acid
Synonyms:
Standard InCHIKey:	RPPYCVULPFKBOG-CSHKLQQTSA-N
Standard InCHI:	InChI=1S/C30H48O2/c1-19(2)22-12-16-30(8)24(28(22,6)15-13-25(31)32)10-9-23-26-21(4)20(3)11-14-27(26,5)17-18-29(23,30)7/h9,20-22,24,26H,1,10-18H2,2-8H3,(H,31,32)/t20-,21+,22+,24-,26+,27-,28+,29-,30-/m1/s1
SMILES:	OC(=O)CC[C@@]1(C)[C@@H](CC[C@@]2([C@@H]1CC=C1[C@@]2(C)CC[C@@]2([C@H]1[C@@H](C)[C@H](C)CC2)C)C)C(=C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3289101
PubChem CID:	12315005
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[9397205]
NPO362	Gentiana crassicaulis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33052051]
NPO33055	boswellia spp.	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24844534]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[22233034]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[16335823]
NPO27	Gentiana dahurica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20352	Gentiana straminea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO362	Gentiana crassicaulis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

Showing 1 to 10 of 24 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
IC50	5
Others	1

Activity Type	# Activity
Individual Protein	6

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT324	Individual Protein	Cyclooxygenase-1	Ovis aries	IC50	>	10000.0	nM	PMID[515806]
NPT31	Individual Protein	Cyclooxygenase-2	Homo sapiens	IC50	>	10000.0	nM	PMID[515806]
NPT956	Individual Protein	Prostaglandin E synthase	Homo sapiens	Activity	=	83.9	%	PMID[515806]
NPT956	Individual Protein	Prostaglandin E synthase	Homo sapiens	IC50	>	10000.0	nM	PMID[515806]

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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 NPC107039 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	178
0.1-0.2	1292
0.2-0.3	6320
0.3-0.4	16288
0.4-0.5	7471
0.5-0.6	5686
0.6-0.7	4015
0.7-0.8	1083
0.8-0.85	278
0.85-0.9	46
0.9-0.95	29
0.95-1	11

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC471897
1.0	High Similarity	NPC471899
0.9861	High Similarity	NPC260385
0.9861	High Similarity	NPC110094
0.9861	High Similarity	NPC280654

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 NPC107039 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	179
0.1-0.2	1670
0.2-0.3	3997
0.3-0.4	2204
0.4-0.5	630
0.5-0.6	244
0.6-0.7	163
0.7-0.8	59
0.8-0.85	4
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
0.8353	Intermediate Similarity	NPD7515	Phase 2
0.8333	Intermediate Similarity	NPD7285	Clinical (unspecified phase)
0.8161	Intermediate Similarity	NPD7748	Approved
0.8	Intermediate Similarity	NPD7513	Clinical (unspecified phase)
0.7952	Intermediate Similarity	NPD4786	Approved

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