NPASS Compound

Structure

CID171888 OpenBabel06191715542D 27 30 0 0 1 0 0 0 0 0999 V2000 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6103 -1.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 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 -4.3301 1.5000 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 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1715 -0.7515 0.0000 C 0 0 1 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 -4.3301 0.5000 0.0000 C 0 0 0 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 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.0860 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5605 -0.7515 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 2 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 0.5000 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 -5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.0860 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3424 -1.3750 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 0.5681 -0.8230 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 8 1 0 0 0 0 2 9 1 0 0 0 0 4 19 1 0 0 0 0 5 8 2 0 0 0 0 5 11 1 0 0 0 0 6 10 1 0 0 0 0 6 12 1 0 0 0 0 7 13 1 0 0 0 0 7 20 1 0 0 0 0 8 10 1 0 0 0 0 9 14 1 0 0 0 0 9 20 1 1 0 0 0 10 18 1 6 0 0 0 11 17 1 0 0 0 0 11 21 2 0 0 0 0 12 19 1 1 0 0 0 12 27 1 0 0 0 0 13 22 2 0 0 0 0 13 27 1 0 0 0 0 14 15 1 0 0 0 0 14 23 1 6 0 0 0 15 16 1 0 0 0 0 15 24 1 6 0 0 0 16 18 1 6 0 0 0 16 19 1 0 0 0 0 17 18 1 6 0 0 0 17 25 1 0 0 0 0 18 3 1 6 0 0 0 19 20 1 1 0 0 0 20 26 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	380.18
Volume:	373.873
LogP:	0.884
LogD:	0.628
LogS:	-3.772
# Rotatable Bonds:	0
TPSA:	121.13
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.406
Synthetic Accessibility Score:	5.369
Fsp3:	0.85
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.11
MDCK Permeability:	5.9185767895542085e-05
Pgp-inhibitor:	0.99
Pgp-substrate:	0.328
Human Intestinal Absorption (HIA):	0.19
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.599

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.855
Plasma Protein Binding (PPB):	33.383277893066406%
Volume Distribution (VD):	0.523
Pgp-substrate:	53.546993255615234%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.626
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.608
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.08
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.093
CYP3A4-inhibitor:	0.091
CYP3A4-substrate:	0.21

ADMET: Excretion

Clearance (CL):	4.443
Half-life (T1/2):	0.504

ADMET: Toxicity

hERG Blockers:	0.042
Human Hepatotoxicity (H-HT):	0.293
Drug-inuced Liver Injury (DILI):	0.267
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.365
Maximum Recommended Daily Dose:	0.131
Skin Sensitization:	0.307
Carcinogencity:	0.516
Eye Corrosion:	0.041
Eye Irritation:	0.017
Respiratory Toxicity:	0.886

Download Data

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

Natural Product: NPC171888

Natural Product ID:	NPC171888
*Common Name:**	QQHDMRQEBBKJIQ-LYLQSLJVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QQHDMRQEBBKJIQ-LYLQSLJVSA-N
Standard InCHI:	InChI=1S/C20H28O7/c1-8-5-11(21)17(25)18(3)10(8)6-12-19(4)16(18)15(24)14(23)9(2)20(19,26)7-13(22)27-12/h5,9-10,12,14-17,23-26H,6-7H2,1-4H3/t9-,10-,12+,14-,15-,16+,17+,18-,19+,20+/m0/s1
SMILES:	O=C1O[C@@H]2C[C@H]3C(=CC(=O)[C@H]([C@@]3([C@@H]3[C@@]2([C@](C1)(O)[C@@H](C)[C@@H]([C@@H]3O)O)C)C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1079670
PubChem CID:	46878938
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0002119] Quassinoids

*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
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25905468]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	n.a.	n.a.	PMID[25066952]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24467387]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919052]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	n.a.	n.a.	PMID[19299148]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	root	n.a.	PMID[1800638]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	Roots	n.a.	n.a.	PMID[14575431]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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
IC50	1

Activity Type	# Activity
Cell Line	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT453	Cell Line	HT-1080	Homo sapiens	IC50	>	100000.0	nM	PMID[479927]

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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 NPC171888 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	251
0.1-0.2	1541
0.2-0.3	4417
0.3-0.4	7387
0.4-0.5	12261
0.5-0.6	7997
0.6-0.7	5243
0.7-0.8	3207
0.8-0.85	289
0.85-0.9	76
0.9-0.95	24
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC146945
0.9808	High Similarity	NPC7921
0.9808	High Similarity	NPC208998
0.9533	High Similarity	NPC97908
0.9533	High Similarity	NPC287343

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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 NPC171888 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	232
0.1-0.2	1827
0.2-0.3	3689
0.3-0.4	2112
0.4-0.5	754
0.5-0.6	284
0.6-0.7	146
0.7-0.8	103
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.844	Intermediate Similarity	NPD5345	Clinical (unspecified phase)
0.8276	Intermediate Similarity	NPD6319	Approved
0.822	Intermediate Similarity	NPD8328	Phase 3
0.8091	Intermediate Similarity	NPD6675	Approved
0.8091	Intermediate Similarity	NPD6402	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