NPASS Compound

Structure

NPC24705 OpenBabel07101718282D 36 40 0 0 1 0 0 0 0 0999 V2000 -4.8363 -2.9680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8997 -5.2985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6428 -5.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1913 -2.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1913 0.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1890 -3.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 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 -3.4980 -4.4543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 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 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8581 -2.7601 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5491 -1.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8289 -5.1974 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 0.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8508 -4.9895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 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 -0.8660 -0.5000 0.0000 C 0 0 2 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 -3.1379 -6.1485 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 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 0.8660 3.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6340 2.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5417 -4.0385 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 25 1 0 0 0 0 3 25 1 0 0 0 0 4 26 1 0 0 0 0 7 10 1 0 0 0 0 7 17 1 0 0 0 0 8 9 1 0 0 0 0 8 19 1 0 0 0 0 9 20 1 0 0 0 0 10 21 1 0 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 27 1 0 0 0 0 13 14 1 0 0 0 0 13 26 1 0 0 0 0 14 29 1 0 0 0 0 15 22 1 0 0 0 0 15 23 1 0 0 0 0 16 29 1 0 0 0 0 17 1 1 1 0 0 0 17 18 1 0 0 0 0 18 26 1 1 0 0 0 19 27 1 6 0 0 0 19 29 1 0 0 0 0 20 28 1 1 0 0 0 20 30 1 0 0 0 0 21 25 1 0 0 0 0 21 31 1 6 0 0 0 22 28 1 1 0 0 0 22 32 1 0 0 0 0 23 30 1 6 0 0 0 23 33 1 0 0 0 0 24 28 1 0 0 0 0 24 34 2 0 0 0 0 24 35 1 0 0 0 0 25 36 1 0 0 0 0 26 27 1 1 0 0 0 27 5 1 6 0 0 0 28 6 1 1 0 0 0 29 30 1 6 0 0 0 30 16 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	506.36
Volume:	534.759
LogP:	2.718
LogD:	2.961
LogS:	-3.897
# Rotatable Bonds:	6
TPSA:	118.22
# H-Bond Aceptor:	6
# H-Bond Donor:	5
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.365
Synthetic Accessibility Score:	5.981
Fsp3:	0.967
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:	-5.835
MDCK Permeability:	1.0212709639745299e-05
Pgp-inhibitor:	0.023
Pgp-substrate:	0.949
Human Intestinal Absorption (HIA):	0.018
20% Bioavailability (F20%):	0.026
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.423
Plasma Protein Binding (PPB):	91.32923126220703%
Volume Distribution (VD):	0.557
Pgp-substrate:	4.9071197509765625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.306
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.719
CYP2C9-inhibitor:	0.034
CYP2C9-substrate:	0.21
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.105
CYP3A4-inhibitor:	0.494
CYP3A4-substrate:	0.196

ADMET: Excretion

Clearance (CL):	2.674
Half-life (T1/2):	0.389

ADMET: Toxicity

hERG Blockers:	0.056
Human Hepatotoxicity (H-HT):	0.632
Drug-inuced Liver Injury (DILI):	0.01
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.882
Maximum Recommended Daily Dose:	0.881
Skin Sensitization:	0.853
Carcinogencity:	0.623
Eye Corrosion:	0.021
Eye Irritation:	0.025
Respiratory Toxicity:	0.985

Download Data

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

Natural Product: NPC24705

Natural Product ID:	NPC24705
*Common Name:**	Quadrangularic Acid L
IUPAC Name:	n.a.
Synonyms:	Quadrangularic Acid L
Standard InCHIKey:	WWIHQMXKPHUIKR-HYVKQYARSA-N
Standard InCHI:	InChI=1S/C30H50O6/c1-17(7-10-21(31)25(2,3)36)18-11-12-27(5)19-8-9-20-28(6,24(34)35)22(32)15-23(33)30(20)16-29(19,30)14-13-26(18,27)4/h17-23,31-33,36H,7-16H2,1-6H3,(H,34,35)/t17-,18-,19+,20+,21-,22+,23+,26-,27+,28+,29+,30-/m1/s1
SMILES:	C[C@H](CC[C@H](C(C)(C)O)O)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4[C@@](C)([C@H](C[C@@H]([C@]54C[C@@]35CC[C@]12C)O)O)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL473039
PubChem CID:	10673183
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols and derivatives

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9934464]
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21265555]
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	leaves	Khon Kaen, Thailand	2006-AUG	PMID[21265555]
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[11277757]
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	seeds	n.a.	n.a.	PMID[10785422]
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10650080]

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☑ 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

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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

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☑ 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
ED50	1

Activity Type	# Activity
NON-MOLECULAR	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	ED50	>	100.0	ug ml-1	PMID[553430]

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☑ 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 NPC24705 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	410
0.1-0.2	3370
0.2-0.3	9018
0.3-0.4	13882
0.4-0.5	5923
0.5-0.6	5398
0.6-0.7	3648
0.7-0.8	914
0.8-0.85	105
0.85-0.9	23
0.9-0.95	2
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC56962
0.9639	High Similarity	NPC302111
0.907	High Similarity	NPC263802
0.9036	High Similarity	NPC12933
0.8953	High Similarity	NPC472272

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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 NPC24705 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	441
0.1-0.2	3592
0.2-0.3	3389
0.3-0.4	1038
0.4-0.5	317
0.5-0.6	229
0.6-0.7	118
0.7-0.8	18
0.8-0.85	4
0.85-0.9	4
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8675	High Similarity	NPD6114	Approved
0.8675	High Similarity	NPD6697	Approved
0.8675	High Similarity	NPD6115	Approved
0.8675	High Similarity	NPD6118	Approved
0.8434	Intermediate Similarity	NPD6117	Approved

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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