NPASS Compound

Structure

NPC145823 OpenBabel06302215282D 36 40 0 0 1 0 0 0 0 0999 V2000 0.1550 1.1777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 0.4878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7462 0.8612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 -0.9756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 -1.4634 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8449 -2.4390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8449 -2.4390 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8449 -4.3902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8449 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 -0.9756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5347 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5347 -2.4390 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3796 -2.9268 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3796 -1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2245 -2.4390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0694 -2.9268 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0694 -3.9024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9143 -4.3902 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2245 -4.3902 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.7123 -5.2351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7367 -5.2351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2245 -6.0800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3796 -3.9024 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5347 -4.3902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 -3.9024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6898 -2.9268 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8449 -3.4146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9143 -2.4390 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9756 0.0000 C 0 0 2 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 -0.8449 0.4878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 -1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6898 -2.9268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5347 -1.4634 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 32 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 31 1 0 0 0 0 6 7 1 0 0 0 0 6 34 1 1 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 28 1 0 0 0 0 9 10 1 6 0 0 0 9 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 14 13 1 1 0 0 0 14 15 1 0 0 0 0 14 28 1 0 0 0 0 15 25 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 30 1 6 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 21 25 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 1 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 1 0 0 0 31 11 1 6 0 0 0 31 32 1 0 0 0 0 32 33 1 6 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	502.33
Volume:	529.486
LogP:	3.601
LogD:	2.704
LogS:	-3.834
# Rotatable Bonds:	2
TPSA:	115.06
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.417
Synthetic Accessibility Score:	5.136
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
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:	-5.44
MDCK Permeability:	1.2631854588107672e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.355

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.847
Plasma Protein Binding (PPB):	88.35077667236328%
Volume Distribution (VD):	0.472
Pgp-substrate:	10.438234329223633%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.243
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.768
CYP2C9-inhibitor:	0.037
CYP2C9-substrate:	0.153
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.104
CYP3A4-inhibitor:	0.182
CYP3A4-substrate:	0.158

ADMET: Excretion

Clearance (CL):	2.506
Half-life (T1/2):	0.602

ADMET: Toxicity

hERG Blockers:	0.009
Human Hepatotoxicity (H-HT):	0.307
Drug-inuced Liver Injury (DILI):	0.022
AMES Toxicity:	0.024
Rat Oral Acute Toxicity:	0.159
Maximum Recommended Daily Dose:	0.162
Skin Sensitization:	0.033
Carcinogencity:	0.032
Eye Corrosion:	0.006
Eye Irritation:	0.017
Respiratory Toxicity:	0.964

Download Data

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

Natural Product: NPC145823

Natural Product ID:	NPC145823
*Common Name:**	LQLFLMUUMZHKFV-QOWVZFTCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LQLFLMUUMZHKFV-QOWVZFTCSA-N
Standard InCHI:	InChI=1S/C30H46O6/c1-25(2)11-13-30(24(35)36)14-12-28(5)17(21(30)23(25)34)7-8-20-26(3)15-18(32)22(33)27(4,16-31)19(26)9-10-29(20,28)6/h7,18-21,23,31-32,34H,8-16H2,1-6H3,(H,35,36)/t18-,19-,20-,21-,23+,26+,27-,28-,29-,30+/m1/s1
SMILES:	CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)C[C@H](C(=O)[C@](C)(CO)[C@@H]5CC[C@@]34C)O)[C@@H]2[C@@H]1O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	53393002
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO18280	Colubrina retusa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[10346942]
NPO18280	Colubrina retusa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[10514332]
NPO19499	Plocamium corallorhiza	Species	Plocamiaceae	Eukaryota	n.a.	South African	n.a.	PMID[17343409]
NPO20674	Pseudopterogorgia rigida	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9090873]
NPO19988	Vinca herbacea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19988	Vinca herbacea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13314	Callitropsis funebris	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20550	Helenium argentinum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19499	Plocamium corallorhiza	Species	Plocamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18280	Colubrina retusa	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20615	Osmites hirsuta	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20217	Vernonanthura squamulosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13314	Callitropsis funebris	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19988	Vinca herbacea	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12448	Simplicillium lamellicola	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22468	Parazoanthus gracilis	Species	Parazoanthidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18112	Melochia chamaedrys	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20674	Pseudopterogorgia rigida	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18639	Breynia vitis-idaea	Species	Phyllanthaceae	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 NPC145823 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	225
0.1-0.2	1446
0.2-0.3	4999
0.3-0.4	12250
0.4-0.5	10472
0.5-0.6	5816
0.6-0.7	4797
0.7-0.8	2245
0.8-0.85	161
0.85-0.9	152
0.9-0.95	132
0.95-1	2

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 NPC145823 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	199
0.1-0.2	1779
0.2-0.3	3786
0.3-0.4	2221
0.4-0.5	707
0.5-0.6	213
0.6-0.7	175
0.7-0.8	65
0.8-0.85	1
0.85-0.9	3
0.9-0.95	1
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