NPASS Compound

Structure

CID281203 OpenBabel06191716092D 33 37 0 0 1 0 0 0 0 0999 V2000 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5981 0.5000 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 1.7321 -2.0000 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 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 0 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 3.4641 0.0000 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 -2.5981 1.5000 0.0000 C 0 0 0 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 0.8660 -1.5000 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 0.0000 -1.0000 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 4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 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 -3.0981 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 0.5000 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 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0981 -0.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 19 1 0 0 0 0 6 29 1 0 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 9 21 1 0 0 0 0 10 11 1 0 0 0 0 10 22 1 0 0 0 0 11 27 1 0 0 0 0 12 13 1 0 0 0 0 12 25 1 0 0 0 0 13 26 1 0 0 0 0 14 16 1 0 0 0 0 14 25 1 0 0 0 0 15 17 1 0 0 0 0 15 28 1 0 0 0 0 16 29 1 0 0 0 0 17 30 1 0 0 0 0 18 23 1 0 0 0 0 18 26 1 0 0 0 0 19 20 1 0 0 0 0 19 27 1 1 0 0 0 20 31 2 0 0 0 0 21 27 1 1 0 0 0 21 28 1 0 0 0 0 22 28 1 1 0 0 0 22 29 1 0 0 0 0 23 25 1 6 0 0 0 23 30 1 0 0 0 0 24 26 1 0 0 0 0 24 32 2 0 0 0 0 24 33 1 0 0 0 0 25 2 1 1 0 0 0 26 3 1 6 0 0 0 27 4 1 1 0 0 0 28 5 1 1 0 0 0 29 30 1 1 0 0 0 30 7 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	456.36
Volume:	505.751
LogP:	6.08
LogD:	4.322
LogS:	-3.872
# Rotatable Bonds:	1
TPSA:	54.37
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.444
Synthetic Accessibility Score:	4.867
Fsp3:	0.933
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:	-5.445
MDCK Permeability:	1.1365379577910062e-05
Pgp-inhibitor:	0.699
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.097
20% Bioavailability (F20%):	0.029
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.386
Plasma Protein Binding (PPB):	90.34587860107422%
Volume Distribution (VD):	0.724
Pgp-substrate:	3.636211633682251%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.629
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.904
CYP2C9-inhibitor:	0.048
CYP2C9-substrate:	0.046
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.583
CYP3A4-substrate:	0.499

ADMET: Excretion

Clearance (CL):	8.358
Half-life (T1/2):	0.142

ADMET: Toxicity

hERG Blockers:	0.041
Human Hepatotoxicity (H-HT):	0.481
Drug-inuced Liver Injury (DILI):	0.031
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.716
Maximum Recommended Daily Dose:	0.57
Skin Sensitization:	0.484
Carcinogencity:	0.592
Eye Corrosion:	0.087
Eye Irritation:	0.02
Respiratory Toxicity:	0.973

Download Data

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

Natural Product: NPC281203

Natural Product ID:	NPC281203
*Common Name:**	(2S,4As,6Ar,6Bs,8As,9R,12As,12Bs,14As,14Br)-2,4A,6A,8A,9,12B,14A-Heptamethyl-10-Oxodocosahydropicene-2-Carboxylic Acid
IUPAC Name:	(2S,4aS,6aS,6aR,6bS,8aS,9R,12aS,14aS,14bR)-2,4a,6a,6a,8a,9,14a-heptamethyl-10-oxo-3,4,5,6,6b,7,8,9,11,12,12a,13,14,14b-tetradecahydro-1H-picene-2-carboxylic acid
Synonyms:
Standard InCHIKey:	WHWHDGKOSUKYOV-VYTNREEISA-N
Standard InCHI:	InChI=1S/C30H48O3/c1-19-20(31)8-9-21-27(19,4)11-10-22-28(21,5)15-17-30(7)23-18-26(3,24(32)33)13-12-25(23,2)14-16-29(22,30)6/h19,21-23H,8-18H2,1-7H3,(H,32,33)/t19-,21+,22-,23+,25+,26-,27+,28-,29+,30-/m0/s1
SMILES:	C[C@H]1C(=O)CC[C@@H]2[C@]1(C)CC[C@H]1[C@@]2(C)CC[C@@]2(C)[C@@H]3C[C@](C)(CC[C@]3(C)CC[C@]12C)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL483029
PubChem CID:	14108946
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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8722541]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8699928]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7304185]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7102323]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31556299]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	Leaves	n.a.	n.a.	PMID[29355322]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	root	n.a.	PMID[2816380]
NPO8412	Monanchora arbuscula	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	PMID[25924111]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	bark	n.a.	PMID[2534610]
NPO13661	Tripterygium wilfordii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25237706]

Showing 1 to 10 of 66 entries

Previous1 2 3 4 5 6 7Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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
ED50	1
IC50	1

Activity Type	# Activity
Cell Line	1
Organism	1

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT759	Cell Line	H9	Homo sapiens	IC50	=	44000.0	nM	PMID[487789]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	ED50	=	59.0	uM	PMID[487789]

Showing 1 to 2 of 2 entries

Previous1Next

☑ 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 NPC281203 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	413
0.1-0.2	4084
0.2-0.3	17180
0.3-0.4	9427
0.4-0.5	5517
0.5-0.6	4215
0.6-0.7	1467
0.7-0.8	343
0.8-0.85	27
0.85-0.9	16
0.9-0.95	4
0.95-1	4

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC100917
1.0	High Similarity	NPC31187
1.0	High Similarity	NPC469724
0.9104	High Similarity	NPC108131
0.9091	High Similarity	NPC2568

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC281203 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	509
0.1-0.2	3872
0.2-0.3	3370
0.3-0.4	848
0.4-0.5	323
0.5-0.6	182
0.6-0.7	21
0.7-0.8	24
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8788	High Similarity	NPD4224	Phase 2
0.8429	Intermediate Similarity	NPD6081	Approved
0.8	Intermediate Similarity	NPD5360	Phase 3
0.8	Intermediate Similarity	NPD5361	Clinical (unspecified phase)
0.7945	Intermediate Similarity	NPD6113	Clinical (unspecified phase)

Showing 1 to 5 of 146 entries

Previous1 2 3 4 5…30Next

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