NPASS Compound

Structure

NPC244053 OpenBabel06302215432D 25 29 0 0 1 0 0 0 0 0999 V2000 1.8440 0.1930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4579 0.8419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8040 0.4643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3010 -0.1042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1663 -0.8472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5015 -1.2052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1929 -0.9086 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -1.1166 -1.0059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4946 -0.1575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8045 0.4642 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4131 0.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2175 -0.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0216 0.4640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0216 1.3930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2176 1.8574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4131 1.3931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6091 1.8575 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8046 1.3932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0001 1.8575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8039 1.3933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.7860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8481 3.1636 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7511 3.3318 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6540 4.2551 0.0000 C 0 0 0 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 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 20 1 0 0 0 0 3 25 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 25 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 1 0 0 0 10 18 1 0 0 0 0 10 11 1 0 0 0 0 10 25 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	338.2
Volume:	355.382
LogP:	3.119
LogD:	3.228
LogS:	-4.208
# Rotatable Bonds:	3
TPSA:	41.9
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.776
Synthetic Accessibility Score:	4.769
Fsp3:	0.619
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.838
MDCK Permeability:	2.5006349460454658e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.986
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.644
30% Bioavailability (F30%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.979
Plasma Protein Binding (PPB):	42.92963409423828%
Volume Distribution (VD):	3.27
Pgp-substrate:	67.47736358642578%

ADMET: Metabolism

CYP1A2-inhibitor:	0.068
CYP1A2-substrate:	0.719
CYP2C19-inhibitor:	0.081
CYP2C19-substrate:	0.942
CYP2C9-inhibitor:	0.081
CYP2C9-substrate:	0.174
CYP2D6-inhibitor:	0.905
CYP2D6-substrate:	0.868
CYP3A4-inhibitor:	0.865
CYP3A4-substrate:	0.72

ADMET: Excretion

Clearance (CL):	7.468
Half-life (T1/2):	0.126

ADMET: Toxicity

hERG Blockers:	0.874
Human Hepatotoxicity (H-HT):	0.561
Drug-inuced Liver Injury (DILI):	0.188
AMES Toxicity:	0.028
Rat Oral Acute Toxicity:	0.864
Maximum Recommended Daily Dose:	0.909
Skin Sensitization:	0.122
Carcinogencity:	0.371
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.955

Download Data

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

Natural Product: NPC244053

Natural Product ID:	NPC244053
*Common Name:**	GIGFIWJRTMBSRP-NJDAHSKKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GIGFIWJRTMBSRP-NJDAHSKKSA-N
Standard InCHI:	InChI=1S/C21H26N2O2/c1-3-20-9-6-11-23-12-10-21(19(20)23)15-7-4-5-8-16(15)22-17(21)14(13-20)18(24)25-2/h4-5,7-8,19,22H,3,6,9-13H2,1-2H3/t19-,20-,21-/m1/s1
SMILES:	CC[C@@]12CCCN3CC[C@]4(c5ccccc5NC4=C(C1)C(=O)OC)[C@@H]23
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	811594
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002755] Aspidospermatan-type alkaloids

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO12216	Gynura elliptica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14590	Ruta oreojasme	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14590	Ruta oreojasme	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25628.1	Abrus pulchellus subsp. cantoniensis	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25599	Gloxinia erinoides	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1409	Drymonia macrophylla	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2065	Eriostemon deserti	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21627	Bambusa chungii	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13490	Diospyros tricolor	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14590	Ruta oreojasme	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14210	Brugmansia arborea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13601	Relicina connivens	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25628.1	Abrus pulchellus subsp. cantoniensis	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19809	Streptomyces roseoviolaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3078	Gentiana pyrenaica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11862	Ostrinia nubilalis	Species	Crambidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12216	Gynura elliptica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6602	Vinca major	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC244053 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	245
0.1-0.2	1028
0.2-0.3	4872
0.3-0.4	18589
0.4-0.5	12416
0.5-0.6	4527
0.6-0.7	808
0.7-0.8	171
0.8-0.85	19
0.85-0.9	5
0.9-0.95	10
0.95-1	7

Similarity Score	Similarity Level	Natural Product ID

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 NPC244053 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	142
0.1-0.2	475
0.2-0.3	785
0.3-0.4	1126
0.4-0.5	3290
0.5-0.6	2802
0.6-0.7	487
0.7-0.8	43
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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