NPASS Compound

Natural Product: NPC472268

Natural Product ID	NPC472268
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Gleditsioside B
IUPAC Name	[(2S,3R,4S,5S,6R)-3-[(2S,3R,4S,5R,6S)-5-[(2S,3R,4S,5R)-3,5-dihydroxy-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-3,4-dihydroxy-6-methyloxan-2-yl]oxy-4,5-dihydroxy-6-[[(2E)-6-hydroxy-2-(hydroxymethyl)-6-methylocta-2,7-dienoyl]oxymethyl]oxan-2-yl] (4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2R,3R,4S,5S,6R)-6-[[(2S,3R,4S,5S)-4,5-dihydroxy-3-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl]oxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3357149
PubChem CID	10701743
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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100225 1 0 101226 1 0 101227 1 0 103228 1 0 105229 1 0 106230 1 0 107231 1 0 108232 1 0 109233 1 0 109234 1 0 111235 1 0 112236 1 0 113237 1 0 114238 1 0 M END

Standard InCHIKey	ORMLQCLBYVIXAG-VNWVVGBMSA-N
Standard InCHI	InChI=1S/C78H124O36/c1-11-74(7,99)18-12-13-34(26-79)63(97)100-31-41-50(88)52(90)62(113-67-57(95)53(91)59(33(2)106-67)110-66-58(96)60(40(83)30-103-66)111-64-54(92)46(84)37(80)27-101-64)70(108-41)114-71(98)78-23-21-72(3,4)25-36(78)35-14-15-44-75(8)19-17-45(73(5,6)43(75)16-20-77(44,10)76(35,9)22-24-78)109-68-56(94)51(89)49(87)42(107-68)32-105-69-61(48(86)39(82)29-104-69)112-65-55(93)47(85)38(81)28-102-65/h11,13-14,33,36-62,64-70,79-96,99H,1,12,15-32H2,2-10H3/b34-13+/t33-,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+,64-,65-,66-,67-,68-,69-,70-,74?,75-,76+,77+,78-/m0/s1
SMILES	CC1C(C(C(C(O1)OC2C(C(C(OC2OC(=O)C34CCC(CC3C5=CCC6C7(CCC(C(C7CCC6(C5(CC4)C)C)(C)C)OC8C(C(C(C(O8)COC9C(C(C(CO9)O)O)OC1C(C(C(CO1)O)O)O)O)O)O)C)(C)C)COC(=O)C(=CCCC(C)(C=C)O)CO)O)O)O)O)OC1C(C(C(CO1)O)OC1C(C(C(CO1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1636.79	Volume:	1558.232 ? Van der Waals volume.
Dense:	1.05	LogP:	-0.354 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.569 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.638 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	25.0	Rigid Bonds:	72.0
TPSA:	556.96 ? Topological Polar Surface Area.	H-Bond Acceptor:	36.0
H-Bond Donor:	19.0	Rings:	12.0
Heavy Atoms:	36.0

MedChem Properties

QED Drug-Likeness Score:	0.02	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.522	Fsp³:	0.897
MCE-18:	263.351 ? 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:	0.031	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.001 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.375 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.411	Promiscuous compounds:	0.005

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.597	MDCK Permeability:	-4.929
Pgp-inhibitor:	0.0	Pgp-substrate:	1.0
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%):	0.999	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	23.667%	Volume Distribution (VD):	-0.377
Fu:	29.223% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.0
OATP1B3 inhibitor:	0.964	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.258	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.186	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.002	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
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):

-1.552

Half-life (T1/2):

5.257

ADMET: Toxicity

hERG Blockers:	0.003	hERG Blockers (10um):	0.3
Human Hepatotoxicity (H-HT):	0.137	Drug-induced Liver Injury (DILI):	0.105
AMES Toxicity:	0.639	Rat Oral Acute Toxicity:	0.017
Maximum Recommended Daily Dose:	0.215	Skin Sensitization:	0.015
Carcinogencity:	0.001	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.183	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.01
Genotoxicity:	0.001	RPMI-8226 Immunitoxicity:	0.122
A549 Cytotoxicity:	0.013	Hek293 Cytotoxicity:	0.979
BCF:	0.277 ? 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:	4.383 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.944 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.521 ? 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
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	anomalous fruits	n.a.	n.a.	PMID[25442304]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20608	Gleditsia sinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20608	Gleditsia sinensis	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

Activity Type	# Activity
Activity	2
IC50	2

Activity Type	# Activity
Cell line	4

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
NPT380	Cell line	U-251	Homo sapiens	Activity	=	32.94	%	PMID[25442304]
NPT76	Cell line	C6	Rattus norvegicus	Activity	=	22.21	%	PMID[24717151]
NPT380	Cell line	U-251	Homo sapiens	IC50	=	44460.0	nM	PMID[25442304]
NPT76	Cell line	C6	Rattus norvegicus	IC50	=	31680.0	nM	PMID[18198839]

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 NPC472268 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	26015
0.1-0.2	20923
0.2-0.3	2035
0.3-0.4	519
0.4-0.5	209
0.5-0.6	106
0.6-0.7	35
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9302	High Similarity	NPC297950
0.8841	High Similarity	NPC472269
0.8231	Intermediate Similarity	NPC224381
0.8154	Intermediate Similarity	NPC70809
0.7986	Intermediate Similarity	NPC23020
0.7945	Intermediate Similarity	NPC472270
0.7945	Intermediate Similarity	NPC112492
0.7319	Intermediate Similarity	NPC102505
0.7319	Intermediate Similarity	NPC488514
0.6985	Remote Similarity	NPC13998
0.6906	Remote Similarity	NPC309223
0.6853	Remote Similarity	NPC480422
0.6765	Remote Similarity	NPC488560
0.6621	Remote Similarity	NPC8524
0.6594	Remote Similarity	NPC85154
0.6575	Remote Similarity	NPC33012
0.6479	Remote Similarity	NPC236638
0.6479	Remote Similarity	NPC294453
0.6331	Remote Similarity	NPC475160
0.6331	Remote Similarity	NPC473714
0.6269	Remote Similarity	NPC481079
0.6224	Remote Similarity	NPC41061
0.6224	Remote Similarity	NPC227551
0.6197	Remote Similarity	NPC57484
0.6169	Remote Similarity	NPC484830
0.6159	Remote Similarity	NPC60557
0.6159	Remote Similarity	NPC67857
0.6145	Remote Similarity	NPC488200
0.6143	Remote Similarity	NPC123199
0.6138	Remote Similarity	NPC305981
0.6138	Remote Similarity	NPC481081
0.6127	Remote Similarity	NPC481080
0.6103	Remote Similarity	NPC295823
0.6103	Remote Similarity	NPC174720
0.6103	Remote Similarity	NPC475467
0.6096	Remote Similarity	NPC261506
0.6096	Remote Similarity	NPC4328
0.6084	Remote Similarity	NPC476068
0.6081	Remote Similarity	NPC250247
0.6028	Remote Similarity	NPC135904
0.6028	Remote Similarity	NPC480419
0.6027	Remote Similarity	NPC202828
0.6027	Remote Similarity	NPC119592
0.6	Remote Similarity	NPC79643
0.5974	Remote Similarity	NPC475177
0.597	Remote Similarity	NPC63159
0.5942	Remote Similarity	NPC104137
0.5942	Remote Similarity	NPC26626
0.5931	Remote Similarity	NPC480418
0.5893	Remote Similarity	NPC488203
0.5878	Remote Similarity	NPC173583
0.5827	Remote Similarity	NPC481078
0.5802	Remote Similarity	NPC475516
0.5793	Remote Similarity	NPC475444
0.5793	Remote Similarity	NPC473679
0.5778	Remote Similarity	NPC488526
0.5765	Remote Similarity	NPC488202
0.5765	Remote Similarity	NPC488204
0.5753	Remote Similarity	NPC473386
0.5743	Remote Similarity	NPC43550
0.5724	Remote Similarity	NPC471577
0.5714	Remote Similarity	NPC286457
0.5704	Remote Similarity	NPC475287
0.5704	Remote Similarity	NPC76972
0.5704	Remote Similarity	NPC469782
0.5704	Remote Similarity	NPC204414
0.5667	Remote Similarity	NPC298034
0.5667	Remote Similarity	NPC71065
0.5643	Remote Similarity	NPC241909
0.564	Remote Similarity	NPC488201
0.5638	Remote Similarity	NPC293330
0.5621	Remote Similarity	NPC480417
0.5608	Remote Similarity	NPC110633
0.5556	Remote Similarity	NPC469946
0.5543	Remote Similarity	NPC174336
0.553	Remote Similarity	NPC48499
0.5529	Remote Similarity	NPC322904
0.5517	Remote Similarity	NPC165204
0.5506	Remote Similarity	NPC475368
0.549	Remote Similarity	NPC220160
0.5482	Remote Similarity	NPC485563
0.5478	Remote Similarity	NPC480421
0.5467	Remote Similarity	NPC471580
0.5461	Remote Similarity	NPC144644
0.5461	Remote Similarity	NPC37860
0.5461	Remote Similarity	NPC170407
0.546	Remote Similarity	NPC45606
0.5419	Remote Similarity	NPC187497
0.5401	Remote Similarity	NPC112352
0.5385	Remote Similarity	NPC469776
0.537	Remote Similarity	NPC484831
0.5368	Remote Similarity	NPC295371
0.5366	Remote Similarity	NPC484829
0.5364	Remote Similarity	NPC470876
0.5364	Remote Similarity	NPC258617
0.5364	Remote Similarity	NPC475514
0.5357	Remote Similarity	NPC297263
0.5333	Remote Similarity	NPC233223
0.5333	Remote Similarity	NPC183816
0.5333	Remote Similarity	NPC220838
0.5329	Remote Similarity	NPC65105
0.5324	Remote Similarity	NPC232237
0.5321	Remote Similarity	NPC68767
0.5321	Remote Similarity	NPC293031
0.5298	Remote Similarity	NPC473452
0.5294	Remote Similarity	NPC136768
0.5294	Remote Similarity	NPC482013
0.5281	Remote Similarity	NPC488513
0.528	Remote Similarity	NPC489208
0.5278	Remote Similarity	NPC31838
0.5278	Remote Similarity	NPC187290
0.5274	Remote Similarity	NPC300419
0.527	Remote Similarity	NPC155410
0.5257	Remote Similarity	NPC481324
0.5254	Remote Similarity	NPC475527
0.5245	Remote Similarity	NPC301449
0.5245	Remote Similarity	NPC601290
0.5238	Remote Similarity	NPC123522
0.5235	Remote Similarity	NPC480423
0.5235	Remote Similarity	NPC100639
0.523	Remote Similarity	NPC324933
0.521	Remote Similarity	NPC196874
0.5172	Remote Similarity	NPC469778
0.5152	Remote Similarity	NPC329893
0.5137	Remote Similarity	NPC815
0.5135	Remote Similarity	NPC192600
0.5133	Remote Similarity	NPC471550
0.5133	Remote Similarity	NPC191827
0.5127	Remote Similarity	NPC478825
0.5118	Remote Similarity	NPC311178
0.5118	Remote Similarity	NPC478559
0.5118	Remote Similarity	NPC478560
0.5115	Remote Similarity	NPC32723
0.5114	Remote Similarity	NPC319719
0.5109	Remote Similarity	NPC235405
0.5108	Remote Similarity	NPC263756
0.5106	Remote Similarity	NPC104400
0.5106	Remote Similarity	NPC10320
0.5106	Remote Similarity	NPC46665
0.5086	Remote Similarity	NPC481323
0.5072	Remote Similarity	NPC249848
0.5072	Remote Similarity	NPC107966
0.507	Remote Similarity	NPC235438
0.5056	Remote Similarity	NPC295941
0.5035	Remote Similarity	NPC104071
0.5035	Remote Similarity	NPC475504
0.5033	Remote Similarity	NPC237191
0.5033	Remote Similarity	NPC470218
0.5029	Remote Similarity	NPC469775
0.5028	Remote Similarity	NPC135334

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472268 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7969
0.1-0.2	1148
0.2-0.3	31
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