NPASS Compound

Structure

NPC111930 OpenBabel06302215352D 23 25 0 0 0 0 0 0 0 0999 V2000 2.8399 2.0992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4060 1.1982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9693 0.3720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5355 -0.5290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5382 -0.6037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1044 -1.5047 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6677 -2.3309 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9749 0.2225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4088 1.1235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9749 2.0245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5984 2.8063 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.2470 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7818 1.6235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6479 2.1235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6479 3.1235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5139 1.6235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5139 0.6235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6479 0.1235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6479 -0.8765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7818 0.6235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3799 2.1235 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0988 -1.3552 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 9 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 23 1 0 0 0 0 5 6 1 0 0 0 0 5 8 2 0 0 0 0 6 7 1 0 0 0 0 8 21 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 20 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 16 2 0 0 0 0 16 17 1 0 0 0 0 16 22 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	694.28
Volume:	684.996
LogP:	2.468
LogD:	1.736
LogS:	-4.016
# Rotatable Bonds:	14
TPSA:	201.17
# H-Bond Aceptor:	15
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.214
Synthetic Accessibility Score:	5.883
Fsp3:	0.647
Lipinski Rule-of-5:	Rejected
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:	-5.269
MDCK Permeability:	0.0001399338070768863
Pgp-inhibitor:	1.0
Pgp-substrate:	0.02
Human Intestinal Absorption (HIA):	0.991
20% Bioavailability (F20%):	0.944
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.091
Plasma Protein Binding (PPB):	43.654541015625%
Volume Distribution (VD):	1.977
Pgp-substrate:	26.06963539123535%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.01
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.014
CYP2D6-inhibitor:	0.915
CYP2D6-substrate:	0.028
CYP3A4-inhibitor:	0.556
CYP3A4-substrate:	0.295

ADMET: Excretion

Clearance (CL):	2.852
Half-life (T1/2):	0.872

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.982
Drug-inuced Liver Injury (DILI):	0.962
AMES Toxicity:	0.042
Rat Oral Acute Toxicity:	0.739
Maximum Recommended Daily Dose:	0.017
Skin Sensitization:	0.062
Carcinogencity:	0.078
Eye Corrosion:	0.948
Eye Irritation:	0.329
Respiratory Toxicity:	0.637

Download Data

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

Natural Product: NPC111930

Natural Product ID:	NPC111930
*Common Name:**	CYTMELDNMYVTKB-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CYTMELDNMYVTKB-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C17H16O6/c1-7-4-12(20)10(6-18)16-13(7)17(21)23-15-9(3)11(19)5-8(2)14(15)22-16/h4-5,18-20H,6H2,1-3H3
SMILES:	Cc1cc(c(CO)c2c1C(=O)Oc1c(C)c(cc(C)c1O2)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46916752
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0001645] Depsides and depsidones

*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
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	stems and leaves	n.a.	n.a.	PMID[18163592]
NPO28178	Artemisia tridentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28560	Sarcomelicope glauca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28407	Clausena heptaphylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28560	Sarcomelicope glauca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28407	Clausena heptaphylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28178	Artemisia tridentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28407	Clausena heptaphylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28108	Stereum princeps	Species	Stereaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28230	Stemona japonica	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28350	Hypsizigus marmoreus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO28407	Clausena heptaphylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23206	Senegalia caffra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29474	Bipolaris victoriae	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28178	Artemisia tridentata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28463	Penicillium gilmanii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28560	Sarcomelicope glauca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27851	Leptothorax muscorum	Species	Formicidae	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 NPC111930 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	384
0.1-0.2	1770
0.2-0.3	4258
0.3-0.4	9679
0.4-0.5	8406
0.5-0.6	3465
0.6-0.7	5151
0.7-0.8	6354
0.8-0.85	2599
0.85-0.9	558
0.9-0.95	59
0.95-1	14

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 NPC111930 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	360
0.1-0.2	1004
0.2-0.3	1914
0.3-0.4	2598
0.4-0.5	1716
0.5-0.6	942
0.6-0.7	423
0.7-0.8	160
0.8-0.85	27
0.85-0.9	6
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