NPASS Compound

Structure

NPC219133 OpenBabel06302215402D 22 22 0 0 1 0 0 0 0 0999 V2000 -1.4042 2.1409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2053 1.2053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9161 0.5652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8258 0.8608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5367 0.2208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3378 -0.7148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4281 -1.0104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0486 -1.3549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8498 -2.2905 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9583 -1.0593 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -0.2956 0.9097 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4783 1.4719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2521 0.9097 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.9565 -0.0000 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 -1.1245 -1.5477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7354 -2.4215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2976 -3.1954 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2159 -2.5215 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1.5188 -0.7738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1297 -1.6477 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4700 -0.6739 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 11 2 1 1 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 20 1 6 0 0 0 15 16 1 1 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 M CHG 2 10 -1 19 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	311.14
Volume:	309.996
LogP:	-0.347
LogD:	4.791
LogS:	-1.679
# Rotatable Bonds:	7
TPSA:	123.93
# H-Bond Aceptor:	7
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.516
Synthetic Accessibility Score:	4.401
Fsp3:	0.533
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.169
MDCK Permeability:	0.00010934232705039904
Pgp-inhibitor:	0.0
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.79
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.2
Plasma Protein Binding (PPB):	57.87406921386719%
Volume Distribution (VD):	0.415
Pgp-substrate:	47.150028228759766%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.028
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.042
CYP2C9-inhibitor:	0.01
CYP2C9-substrate:	0.808
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.123
CYP3A4-inhibitor:	0.013
CYP3A4-substrate:	0.008

ADMET: Excretion

Clearance (CL):	1.213
Half-life (T1/2):	0.784

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.348
Drug-inuced Liver Injury (DILI):	0.176
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.241
Maximum Recommended Daily Dose:	0.786
Skin Sensitization:	0.246
Carcinogencity:	0.348
Eye Corrosion:	0.004
Eye Irritation:	0.022
Respiratory Toxicity:	0.304

Download Data

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

Natural Product: NPC219133

Natural Product ID:	NPC219133
*Common Name:**	DDAJBUQQWFXHDM-HKHGPXCKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DDAJBUQQWFXHDM-HKHGPXCKSA-N
Standard InCHI:	InChI=1S/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h4-5,10-11,13,16H,3,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/p-2/b8-4+,9-5+/t10-,11+,13-/m0/s1
SMILES:	C/C(=CC/C=C(C)/C(=O)[O-])/[C@H]1CN[C@@H]([C@H]1CC(=O)[O-])C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6442550
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0001801] Kainoids

*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
NPO28122	Senecio chionophilus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15387646]
NPO12214	Leontice robustum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28645	Chondria armata	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12214	Leontice robustum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28645	Chondria armata	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12214	Leontice robustum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28122	Senecio chionophilus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28082	Corydalis tashiroi	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28522	Flustra denticulata	Species	Flustridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28105	Coriolopsis gallica	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28331	Astragalus siculus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27701	Otholobium glandulosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28493	Euphorbia cuneata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28539	Xestospongia vanilla	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21945	Amomum melegueta	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27768	Terminalia brachystemma	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28314	Hakea trifurcata	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27849	Raoulia australis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28645	Chondria armata	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27917	Ulmus campestris	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28505	Arum palaestinum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12214	Leontice robustum	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28279	Mikania cordifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28030	Polysiphonia nigra	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28227	Prunus speciosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27889	Anacyclus monanthos	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28403	Comanthus bennetti	Species	Comatulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28420	Guizotia scabra	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27969	Elvira biflora	Species	Trochilidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28156	Nezara viridula	Species	Pentatomidae	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 NPC219133 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	78
0.1-0.2	726
0.2-0.3	14812
0.3-0.4	18708
0.4-0.5	7501
0.5-0.6	824
0.6-0.7	45
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	1
0.95-1	0

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 NPC219133 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	78
0.1-0.2	469
0.2-0.3	3561
0.3-0.4	3802
0.4-0.5	1102
0.5-0.6	128
0.6-0.7	10
0.7-0.8	0
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