NPASS Compound

Natural Product: NPC482013

Natural Product ID	NPC482013
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PEXFWZVVZDIHIL-XVFJOPLNSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	90664258
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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112233 1 1 113234 1 0 113235 1 0 114236 1 0 116237 1 0 117238 1 0 M END

Standard InCHIKey	PEXFWZVVZDIHIL-XVFJOPLNSA-N
Standard InCHI	InChI=1S/C80H121NO36/c1-33-63(113-69-60(99)54(93)42(29-84)108-69)64(114-70-61(100)57(96)52(91)40(27-82)107-70)62(101)71(106-33)116-66-58(97)53(92)41(28-83)109-73(66)117-74(102)80-24-23-78(8)36(37(80)25-75(3,4)47(26-80)111-48(88)18-15-35-13-11-10-12-14-35)16-17-45-77(7)21-20-46(76(5,6)44(77)19-22-79(45,78)9)112-67-49(81-34(2)85)56(95)55(94)43(110-67)32-105-72-65(51(90)39(87)31-104-72)115-68-59(98)50(89)38(86)30-103-68/h10-16,18,33,37-47,49-73,82-84,86-87,89-101H,17,19-32H2,1-9H3,(H,81,85)/b18-15+/t33-,37-,38+,39-,40-,41-,42-,43-,44-,45+,46-,47-,49-,50-,51+,52+,53+,54-,55+,56+,57-,58-,59-,60+,61-,62+,63-,64+,65-,66-,67-,68-,69-,70-,71-,72-,73-,77-,78+,79+,80+/m0/s1
SMILES	C[C@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O[C@H]1[C@H]([C@@H]([C@H](CO)O[C@H]1OC(=O)[C@]12CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)O[C@H]3[C@H]([C@H]([C@@H]([C@H](CO[C@H]4[C@H]([C@@H]([C@H](CO4)O)O)O[C@H]4[C@H]([C@H]([C@@H](CO4)O)O)O)O3)O)O)N=C(C)O)[C@@H]2CC(C)(C)[C@H](C1)OC(=O)/C=C/c1ccccc1)O)O)O)O[C@H]1[C@H]([C@H]([C@@H]([C@H](CO)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@H](CO)O1)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1671.77	Volume:	1587.355 ? Van der Waals volume.
Dense:	1.053	LogP:	-0.342 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.705 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.169 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	24.0	Rigid Bonds:	77.0
TPSA:	569.32 ? Topological Polar Surface Area.	H-Bond Acceptor:	37.0
H-Bond Donor:	19.0	Rings:	13.0
Heavy Atoms:	37.0

MedChem Properties

QED Drug-Likeness Score:	0.013	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.569	Fsp³:	0.838
MCE-18:	369.735 ? 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:	0.984	Fluc inhibitor:	0.314 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.152 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.02 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.294	Promiscuous compounds:	0.014

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-7.485	MDCK Permeability:	-4.83
Pgp-inhibitor:	0.0	Pgp-substrate:	0.998
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%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.379
Plasma Protein Binding (PPB):	61.176%	Volume Distribution (VD):	-0.331
Fu:	20.015% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.715	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:	0.965	CYP3A4-substrate:	0.984
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
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):

-0.689

Half-life (T1/2):

3.509

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.997	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	1.0	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:	0.96	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	0.532	RPMI-8226 Immunitoxicity:	0.571
A549 Cytotoxicity:	0.999	Hek293 Cytotoxicity:	0.741
BCF:	0.32 ? 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:	3.904 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.252 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.952 ? 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
NPO9900	Enterolobium contortisiliquum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12639544]
NPO9900	Enterolobium contortisiliquum	Species	Fabaceae	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	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

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

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 NPC482013 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	20218
0.1-0.2	25877
0.2-0.3	2773
0.3-0.4	599
0.4-0.5	287
0.5-0.6	79
0.6-0.7	19
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	Natural Product ID
0.7125	Intermediate Similarity	NPC488620
0.6626	Remote Similarity	NPC113620
0.6545	Remote Similarity	NPC100612
0.6541	Remote Similarity	NPC220838
0.65	Remote Similarity	NPC13989
0.645	Remote Similarity	NPC488200
0.6442	Remote Similarity	NPC488618
0.6405	Remote Similarity	NPC120667
0.6405	Remote Similarity	NPC278272
0.6402	Remote Similarity	NPC488619
0.6391	Remote Similarity	NPC265699
0.6301	Remote Similarity	NPC174336
0.6273	Remote Similarity	NPC45606
0.6234	Remote Similarity	NPC489209
0.6203	Remote Similarity	NPC489208
0.6158	Remote Similarity	NPC187497
0.6101	Remote Similarity	NPC475177
0.6069	Remote Similarity	NPC488202
0.6042	Remote Similarity	NPC210729
0.6042	Remote Similarity	NPC82931
0.5974	Remote Similarity	NPC70809
0.593	Remote Similarity	NPC322904
0.5904	Remote Similarity	NPC300655
0.5904	Remote Similarity	NPC196874
0.589	Remote Similarity	NPC484830
0.5852	Remote Similarity	NPC488201
0.5829	Remote Similarity	NPC488203
0.5793	Remote Similarity	NPC484831
0.5765	Remote Similarity	NPC222951
0.5722	Remote Similarity	NPC476113
0.5676	Remote Similarity	NPC172365
0.5655	Remote Similarity	NPC233223
0.5655	Remote Similarity	NPC183816
0.5655	Remote Similarity	NPC43589
0.564	Remote Similarity	NPC475444
0.564	Remote Similarity	NPC473679
0.5618	Remote Similarity	NPC488204
0.5616	Remote Similarity	NPC481079
0.5602	Remote Similarity	NPC40085
0.5595	Remote Similarity	NPC484829
0.5536	Remote Similarity	NPC264270
0.5535	Remote Similarity	NPC224381
0.5523	Remote Similarity	NPC311178
0.5506	Remote Similarity	NPC319719
0.5503	Remote Similarity	NPC329878
0.548	Remote Similarity	NPC469778
0.5436	Remote Similarity	NPC207738
0.5385	Remote Similarity	NPC57484
0.5385	Remote Similarity	NPC469946
0.5355	Remote Similarity	NPC295941
0.5342	Remote Similarity	NPC63159
0.5304	Remote Similarity	NPC481324
0.5294	Remote Similarity	NPC472268
0.5294	Remote Similarity	NPC329893
0.5278	Remote Similarity	NPC324933
0.5274	Remote Similarity	NPC480475
0.525	Remote Similarity	NPC111466
0.5235	Remote Similarity	NPC297950
0.5226	Remote Similarity	NPC135904
0.5226	Remote Similarity	NPC123199
0.5212	Remote Similarity	NPC480422
0.5206	Remote Similarity	NPC475649
0.5197	Remote Similarity	NPC280941
0.5197	Remote Similarity	NPC235772
0.5181	Remote Similarity	NPC33012
0.517	Remote Similarity	NPC232237
0.517	Remote Similarity	NPC478559
0.517	Remote Similarity	NPC478560
0.5167	Remote Similarity	NPC32723
0.5165	Remote Similarity	NPC135334
0.5157	Remote Similarity	NPC480418
0.5157	Remote Similarity	NPC286457
0.5153	Remote Similarity	NPC488212
0.5138	Remote Similarity	NPC481323
0.5132	Remote Similarity	NPC104137
0.5132	Remote Similarity	NPC26626
0.5132	Remote Similarity	NPC481078
0.5127	Remote Similarity	NPC488211
0.5125	Remote Similarity	NPC41061
0.5125	Remote Similarity	NPC227551
0.512	Remote Similarity	NPC8524
0.5101	Remote Similarity	NPC297263
0.5097	Remote Similarity	NPC123522
0.5097	Remote Similarity	NPC79643
0.5062	Remote Similarity	NPC236638
0.5062	Remote Similarity	NPC294453
0.5062	Remote Similarity	NPC305981
0.5062	Remote Similarity	NPC481081
0.5061	Remote Similarity	NPC482010
0.5034	Remote Similarity	NPC112352
0.5033	Remote Similarity	NPC187290
0.5032	Remote Similarity	NPC60557
0.5032	Remote Similarity	NPC200788
0.5032	Remote Similarity	NPC67857
0.5032	Remote Similarity	NPC603137
0.5031	Remote Similarity	NPC261506
0.5031	Remote Similarity	NPC4328
0.503	Remote Similarity	NPC250247
0.5027	Remote Similarity	NPC469772

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC482013 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5537
0.1-0.2	3580
0.2-0.3	32
0.3-0.4	1
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