NPASS Compound

Structure

CID49597 OpenBabel06191715382D 36 39 0 0 1 0 0 0 0 0999 V2000 2.5602 2.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3738 -1.4855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5328 -0.1984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8386 0.1617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1170 -2.1547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2760 -0.8675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0465 1.1399 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 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2024 3.0827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5817 -0.5074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0680 -1.8457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2079 2.9781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3034 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 1 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 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6092 2.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8112 -2.5148 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4612 3.7213 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5113 2.7872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 2.1045 0.0000 O 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 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3523 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 5 1 0 0 0 0 2 12 2 0 0 0 0 3 6 2 0 0 0 0 3 12 1 0 0 0 0 4 7 2 0 0 0 0 4 12 1 0 0 0 0 5 13 2 0 0 0 0 6 13 1 0 0 0 0 7 16 1 0 0 0 0 8 9 2 0 0 0 0 8 24 1 0 0 0 0 9 33 1 0 0 0 0 10 15 1 0 0 0 0 10 23 1 0 0 0 0 11 25 1 0 0 0 0 13 26 1 0 0 0 0 14 11 1 1 0 0 0 14 17 1 0 0 0 0 14 34 1 0 0 0 0 15 24 1 6 0 0 0 15 27 1 0 0 0 0 16 28 2 0 0 0 0 16 36 1 0 0 0 0 17 18 1 0 0 0 0 17 29 1 6 0 0 0 18 19 1 0 0 0 0 18 30 1 1 0 0 0 19 21 1 0 0 0 0 19 31 1 6 0 0 0 20 22 1 0 0 0 0 20 23 1 1 0 0 0 20 24 1 0 0 0 0 21 34 1 0 0 0 0 21 35 1 1 0 0 0 22 33 1 0 0 0 0 22 35 1 6 0 0 0 23 1 1 1 0 0 0 23 36 1 0 0 0 0 24 32 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	510.17
Volume:	479.098
LogP:	0.404
LogD:	-0.222
LogS:	-2.68
# Rotatable Bonds:	7
TPSA:	195.6
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.173
Synthetic Accessibility Score:	4.946
Fsp3:	0.542
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:	-6.379
MDCK Permeability:	5.626748315989971e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.953
Human Intestinal Absorption (HIA):	0.48
20% Bioavailability (F20%):	0.876
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.149
Plasma Protein Binding (PPB):	68.65837860107422%
Volume Distribution (VD):	0.389
Pgp-substrate:	29.894760131835938%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.081
CYP2C19-inhibitor:	0.019
CYP2C19-substrate:	0.067
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.11
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.123
CYP3A4-inhibitor:	0.203
CYP3A4-substrate:	0.064

ADMET: Excretion

Clearance (CL):	1.155
Half-life (T1/2):	0.764

ADMET: Toxicity

hERG Blockers:	0.049
Human Hepatotoxicity (H-HT):	0.192
Drug-inuced Liver Injury (DILI):	0.027
AMES Toxicity:	0.069
Rat Oral Acute Toxicity:	0.393
Maximum Recommended Daily Dose:	0.361
Skin Sensitization:	0.606
Carcinogencity:	0.884
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC49597

Natural Product ID:	NPC49597
*Common Name:**	8-Coumaroylharpagide
IUPAC Name:	[(1S,4aS,5R,7S,7aS)-4a,5-dihydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,5,6,7a-tetrahydrocyclopenta[c]pyran-7-yl] (E)-3-(4-hydroxyphenyl)prop-2-enoate
Synonyms:	8-Coumaroylharpagide
Standard InCHIKey:	AZKQDXZMKREFDY-CBLWINFVSA-N
Standard InCHI:	InChI=1S/C24H30O12/c1-23(36-16(28)7-4-12-2-5-13(26)6-3-12)10-15(27)24(32)8-9-33-22(20(23)24)35-21-19(31)18(30)17(29)14(11-25)34-21/h2-9,14-15,17-22,25-27,29-32H,10-11H2,1H3/b7-4+/t14-,15-,17-,18+,19-,20-,21+,22+,23+,24-/m1/s1
SMILES:	OC[C@H]1O[C@@H](O[C@@H]2OC=C[C@@]3([C@H]2[C@@](C)(OC(=O)/C=C/c2ccc(cc2)O)C[C@H]3O)O)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL513852
PubChem CID:	10324058
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-glycosides

*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
NPO5565	Harpagophytum procumbens	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5565	Harpagophytum procumbens	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5565	Harpagophytum procumbens	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

Showing 1 to 3 of 3 entries

Previous1Next

☑ 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
Others	1

Activity Type	# Activity
Organism	1

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2688	Organism	Sus scrofa	Sus scrofa	Inhibition	<	50.0	%	PMID[503818]

Showing 1 to 1 of 1 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 NPC49597 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	285
0.1-0.2	1150
0.2-0.3	2856
0.3-0.4	6745
0.4-0.5	10788
0.5-0.6	10967
0.6-0.7	8394
0.7-0.8	1312
0.8-0.85	135
0.85-0.9	33
0.9-0.95	22
0.95-1	10

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.9701	High Similarity	NPC46644
0.9559	High Similarity	NPC263397
0.9559	High Similarity	NPC302286
0.9559	High Similarity	NPC88754
0.9559	High Similarity	NPC116104

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 NPC49597 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	230
0.1-0.2	714
0.2-0.3	1655
0.3-0.4	2915
0.4-0.5	2169
0.5-0.6	1205
0.6-0.7	247
0.7-0.8	14
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
0.8194	Intermediate Similarity	NPD7266	Discontinued
0.8137	Intermediate Similarity	NPD7685	Pre-registration
0.7662	Intermediate Similarity	NPD1653	Approved
0.75	Intermediate Similarity	NPD1091	Approved
0.7315	Intermediate Similarity	NPD6653	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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