NPASS Compound

Natural Product: NPC484831

Natural Product ID	NPC484831
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JHZVFJMFGDOVNY-LCKSLHJQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	24770289
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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Standard InCHIKey	JHZVFJMFGDOVNY-LCKSLHJQSA-N
Standard InCHI	InChI=1S/C80H128O39/c1-31(18-21-81)12-11-13-34(25-82)66(103)113-46-24-80(74(104)119-73-65(56(97)50(91)39(27-84)111-73)118-71-61(102)63(116-70-60(101)53(94)49(90)38(26-83)109-70)62(33(3)108-71)115-69-58(99)51(92)40(28-85)110-69)36(22-75(46,4)5)35-14-15-43-77(8)19-17-45(76(6,7)42(77)16-20-78(43,9)79(35,10)23-44(80)87)114-68-59(100)54(95)52(93)41(112-68)30-106-72-64(55(96)47(88)32(2)107-72)117-67-57(98)48(89)37(86)29-105-67/h13-14,18,32-33,36-65,67-73,81-102H,11-12,15-17,19-30H2,1-10H3/b31-18+,34-13+/t32-,33+,36+,37-,38-,39-,40+,41-,42+,43-,44-,45+,46+,47+,48+,49-,50-,51+,52-,53+,54+,55+,56+,57-,58-,59-,60-,61-,62+,63+,64-,65-,67+,68+,69+,70+,71+,72-,73+,77+,78-,79-,80-/m1/s1
SMILES	C/C(=CCO)/CC/C=C(CO)/C(=O)O[C@H]1C[C@]2([C@@H](CC1(C)C)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@H]([C@@H](C)O2)O)O)O[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O1)O)O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O[C@H]1[C@@H]([C@H]([C@H](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1712.8	Volume:	1619.194 ? Van der Waals volume.
Dense:	1.058	LogP:	-0.353 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.805 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.116 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	27.0	Rigid Bonds:	71.0
TPSA:	617.65 ? Topological Polar Surface Area.	H-Bond Acceptor:	39.0
H-Bond Donor:	22.0	Rings:	12.0
Heavy Atoms:	39.0

MedChem Properties

QED Drug-Likeness Score:	0.018	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.801	Fsp³:	0.9
MCE-18:	265.632 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.715	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.442	Promiscuous compounds:	0.184

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-7.135	MDCK Permeability:	-4.84
Pgp-inhibitor:	0.0	Pgp-substrate:	0.029
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	1.0
20% Bioavailability (F20%):	0.452	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.0
Plasma Protein Binding (PPB):	56.709%	Volume Distribution (VD):	-0.274
Fu:	19.304% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.035
HLM stability:	0.0 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

-1.566

Half-life (T1/2):

5.038

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.756	Drug-induced Liver Injury (DILI):	0.988
AMES Toxicity:	0.997	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.001	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.869	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	0.047	RPMI-8226 Immunitoxicity:	0.603
A549 Cytotoxicity:	0.982	Hek293 Cytotoxicity:	0.368
BCF:	0.397 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.464 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.474 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.153 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO40910	Pithecellobium lucidum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[18095653]
NPO40910	Pithecellobium lucidum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]

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	Organism Name	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
IC50	5

Activity Type	# Activity
Cell line	5

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT180	Cell line	HCT-8	Homo sapiens	IC50	=	4240.0	nM	PMID[18095653]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	=	7560.0	nM	PMID[18095653]
NPT547	Cell line	BGC-823	Homo sapiens	IC50	>	10000.0	nM	PMID[18095653]
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[18095653]
NPT179	Cell line	A2780	Homo sapiens	IC50	=	1660.0	nM	PMID[18095653]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC484831 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	24199
0.1-0.2	22114
0.2-0.3	2452
0.3-0.4	647
0.4-0.5	320
0.5-0.6	72
0.6-0.7	24
0.7-0.8	0
0.8-0.85	3
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8788	High Similarity	NPC484830
0.8529	High Similarity	NPC233223
0.8529	High Similarity	NPC183816
0.8456	Intermediate Similarity	NPC484829
0.8071	Intermediate Similarity	NPC196874
0.8	Intermediate Similarity	NPC43589
0.7883	Intermediate Similarity	NPC475177
0.7838	Intermediate Similarity	NPC324933
0.7778	Intermediate Similarity	NPC311178
0.7687	Intermediate Similarity	NPC113620
0.7584	Intermediate Similarity	NPC100612
0.7569	Intermediate Similarity	NPC300655
0.7434	Intermediate Similarity	NPC319719
0.7365	Intermediate Similarity	NPC222951
0.7303	Intermediate Similarity	NPC322904
0.7211	Intermediate Similarity	NPC13989
0.72	Intermediate Similarity	NPC475444
0.72	Intermediate Similarity	NPC473679
0.7152	Intermediate Similarity	NPC174336
0.7075	Intermediate Similarity	NPC45606
0.6975	Remote Similarity	NPC187497
0.6959	Remote Similarity	NPC329878
0.6943	Remote Similarity	NPC265699
0.6905	Remote Similarity	NPC105800
0.6846	Remote Similarity	NPC207738
0.6752	Remote Similarity	NPC488620
0.6711	Remote Similarity	NPC329893
0.6689	Remote Similarity	NPC220838
0.6687	Remote Similarity	NPC488204
0.6623	Remote Similarity	NPC478559
0.6623	Remote Similarity	NPC478560
0.6519	Remote Similarity	NPC123522
0.6341	Remote Similarity	NPC488201
0.6319	Remote Similarity	NPC488203
0.6308	Remote Similarity	NPC232237
0.6197	Remote Similarity	NPC286457
0.6125	Remote Similarity	NPC488619
0.6118	Remote Similarity	NPC489208
0.6067	Remote Similarity	NPC33012
0.6062	Remote Similarity	NPC488618
0.6042	Remote Similarity	NPC470876
0.604	Remote Similarity	NPC489209
0.6027	Remote Similarity	NPC309223
0.6	Remote Similarity	NPC8524
0.5988	Remote Similarity	NPC488202
0.5985	Remote Similarity	NPC104137
0.5985	Remote Similarity	NPC26626
0.5973	Remote Similarity	NPC102505
0.5973	Remote Similarity	NPC488514
0.5899	Remote Similarity	NPC172365
0.5828	Remote Similarity	NPC23020
0.5793	Remote Similarity	NPC482013
0.5753	Remote Similarity	NPC473452
0.5753	Remote Similarity	NPC13998
0.5733	Remote Similarity	NPC220160
0.5724	Remote Similarity	NPC85154
0.5667	Remote Similarity	NPC70809
0.5665	Remote Similarity	NPC488513
0.5629	Remote Similarity	NPC472270
0.5629	Remote Similarity	NPC112492
0.5625	Remote Similarity	NPC603137
0.5614	Remote Similarity	NPC488200
0.5612	Remote Similarity	NPC481079
0.5588	Remote Similarity	NPC164389
0.5588	Remote Similarity	NPC488526
0.5507	Remote Similarity	NPC488517
0.5455	Remote Similarity	NPC185466
0.5425	Remote Similarity	NPC482010
0.5417	Remote Similarity	NPC610204
0.5385	Remote Similarity	NPC210729
0.5385	Remote Similarity	NPC82931
0.5379	Remote Similarity	NPC1046
0.537	Remote Similarity	NPC472268
0.5362	Remote Similarity	NPC148603
0.5325	Remote Similarity	NPC224381
0.5316	Remote Similarity	NPC480421
0.5302	Remote Similarity	NPC4749
0.5298	Remote Similarity	NPC475514
0.529	Remote Similarity	NPC250247
0.5287	Remote Similarity	NPC480422
0.527	Remote Similarity	NPC283417
0.527	Remote Similarity	NPC200049
0.5267	Remote Similarity	NPC473386
0.5252	Remote Similarity	NPC305267
0.5211	Remote Similarity	NPC37134
0.5205	Remote Similarity	NPC473824
0.5205	Remote Similarity	NPC610461
0.5203	Remote Similarity	NPC135904
0.5166	Remote Similarity	NPC21691
0.5148	Remote Similarity	NPC485563
0.5143	Remote Similarity	NPC173859
0.5139	Remote Similarity	NPC295823
0.5139	Remote Similarity	NPC174720
0.5139	Remote Similarity	NPC475467
0.5133	Remote Similarity	NPC471577
0.513	Remote Similarity	NPC136768
0.5106	Remote Similarity	NPC63159
0.5101	Remote Similarity	NPC123199
0.5101	Remote Similarity	NPC609305
0.5099	Remote Similarity	NPC481080
0.5097	Remote Similarity	NPC302543
0.5072	Remote Similarity	NPC470512
0.507	Remote Similarity	NPC123796
0.507	Remote Similarity	NPC470513
0.5069	Remote Similarity	NPC606145
0.5068	Remote Similarity	NPC815
0.5068	Remote Similarity	NPC606553
0.5067	Remote Similarity	NPC475140
0.5036	Remote Similarity	NPC469946
0.5035	Remote Similarity	NPC484832
0.5034	Remote Similarity	NPC470911
0.5033	Remote Similarity	NPC265841
0.5033	Remote Similarity	NPC480418
0.5032	Remote Similarity	NPC236638
0.5032	Remote Similarity	NPC294453
0.5032	Remote Similarity	NPC305981

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC484831 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7869
0.1-0.2	1245
0.2-0.3	34
0.3-0.4	2
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
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
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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