NPASS Compound

Structure

NPC113691 OpenBabel06302215392D 47 50 0 0 1 0 0 0 0 0999 V2000 10.4360 2.8442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5776 3.3571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7042 2.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8457 3.3830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9723 2.8960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1139 3.4089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2404 2.9219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3820 3.4348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5086 2.9478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6501 3.4607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7767 2.9738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9183 3.4867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0449 2.9997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8136 3.5126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6870 3.0256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7019 2.0257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5753 1.5387 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8435 1.5128 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8584 0.5129 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7319 0.0259 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5903 0.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7468 -0.9740 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8884 -1.4869 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7541 -2.4778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4452 -3.2006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4412 -3.1110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9921 -2.2764 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6831 -1.3254 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4921 -0.7376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3011 -1.3254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2521 -1.0163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9921 -2.2764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5799 -3.0854 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2232 -2.9158 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0938 -4.1369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1073 -4.3007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0150 -0.9999 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8584 -0.5129 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7319 -0.0259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7169 -1.0258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5903 -0.5388 0.0000 O 0 0 0 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 0.0150 0.9999 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8884 1.4869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9033 2.4868 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7468 0.9740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3265 -1.8813 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 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 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 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 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 42 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 22 28 1 0 0 0 0 22 23 1 0 0 0 0 22 47 1 0 0 0 0 23 24 1 0 0 0 0 23 37 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 35 1 0 0 0 0 26 27 1 0 0 0 0 27 32 1 0 0 0 0 27 28 1 0 0 0 0 27 34 1 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 30 32 1 0 0 0 0 32 33 2 0 0 0 0 35 36 1 0 0 0 0 37 38 1 0 0 0 0 37 42 1 0 0 0 0 38 39 1 0 0 0 0 38 40 1 0 0 0 0 38 42 1 0 0 0 0 40 41 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	660.42
Volume:	697.508
LogP:	6.428
LogD:	3.933
LogS:	-4.367
# Rotatable Bonds:	20
TPSA:	150.59
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.085
Synthetic Accessibility Score:	5.202
Fsp3:	0.816
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.854
MDCK Permeability:	2.9274006010382436e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.701
Human Intestinal Absorption (HIA):	0.118
20% Bioavailability (F20%):	0.998
30% Bioavailability (F30%):	0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.567
Plasma Protein Binding (PPB):	96.26078033447266%
Volume Distribution (VD):	1.368
Pgp-substrate:	2.9708688259124756%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.117
CYP2C19-inhibitor:	0.314
CYP2C19-substrate:	0.132
CYP2C9-inhibitor:	0.555
CYP2C9-substrate:	0.077
CYP2D6-inhibitor:	0.018
CYP2D6-substrate:	0.008
CYP3A4-inhibitor:	0.937
CYP3A4-substrate:	0.105

ADMET: Excretion

Clearance (CL):	3.88
Half-life (T1/2):	0.081

ADMET: Toxicity

hERG Blockers:	0.693
Human Hepatotoxicity (H-HT):	0.946
Drug-inuced Liver Injury (DILI):	0.559
AMES Toxicity:	0.034
Rat Oral Acute Toxicity:	0.877
Maximum Recommended Daily Dose:	0.906
Skin Sensitization:	0.907
Carcinogencity:	0.118
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.981

Download Data

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

Natural Product: NPC113691

Natural Product ID:	NPC113691
*Common Name:**	DYHBGVHTKOPQDM-SGPTVBMASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DYHBGVHTKOPQDM-SGPTVBMASA-N
Standard InCHI:	InChI=1S/C38H60O9/c1-6-7-8-9-10-11-12-13-14-15-16-17-18-19-31(42)46-34-26(3)37(45)29(32-35(5,24-40)38(32,34)47-27(4)41)21-28(23-39)22-36(44)30(37)20-25(2)33(36)43/h20-21,26,29-30,32,34,39-40,44-45H,6-19,22-24H2,1-5H3/t26-,29+,30-,32-,34-,35-,36-,37-,38-/m1/s1
SMILES:	CCCCCCCCCCCCCCCC(=O)O[C@@H]1[C@@H](C)[C@]2([C@@H](C=C(C[C@]3([C@H]2C=C(C)C3=O)O)CO)[C@@H]2[C@@](C)(CO)[C@]12OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	334044
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0002875] Tigliane and ingenane diterpenoids [CHEMONTID:0002906] Phorbol esters

*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
NPO28169	Aleurites cordata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28169	Aleurites cordata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28169	Aleurites cordata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28169	Aleurites cordata	Species	Euphorbiaceae	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

Activity Type	# Activity
Others	7

Activity Type	# Activity
Organism	7

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT747	Organism	Acinetobacter baumannii	Acinetobacter baumannii	Inhibition	=	-9.19	%	PMID[540232]
NPT19	Organism	Escherichia coli	Escherichia coli	Inhibition	=	2.92	%	PMID[540232]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	Inhibition	=	11.05	%	PMID[540232]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Inhibition	=	9.28	%	PMID[540232]
NPT20	Organism	Candida albicans	Candida albicans	Inhibition	=	-4.72	%	PMID[540232]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	Inhibition	=	-11.83	%	PMID[540232]
NPT2922	Organism	Staphylococcus aureus subsp. aureus	Staphylococcus aureus subsp. aureus	Inhibition	=	18.67	%	PMID[540232]

☑ 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 NPC113691 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	248
0.1-0.2	1483
0.2-0.3	4493
0.3-0.4	7418
0.4-0.5	13814
0.5-0.6	7902
0.6-0.7	5885
0.7-0.8	1300
0.8-0.85	30
0.85-0.9	30
0.9-0.95	54
0.95-1	40

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 NPC113691 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	220
0.1-0.2	1952
0.2-0.3	3682
0.3-0.4	2112
0.4-0.5	771
0.5-0.6	242
0.6-0.7	158
0.7-0.8	13
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