NPASS Compound

Natural Product: NPC264270

Natural Product ID	NPC264270
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Pachyelaside C
IUPAC Name	(3S,4aR,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2R,3R,4S,5S,6R)-3-[(2S,3R,4S,5R)-4-[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-3,5-dihydroxyoxan-2-yl]oxy-4-hydroxy-6-(hydroxymethyl)-5-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-2,2,6a,6b,9,9,12a-heptamethyl-3-[(E)-3-phenylprop-2-enoyl]oxy-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2252210
PubChem CID	76319153
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

RDKit 2D 195205 0 0 0 0 0 0 0 0999 V2000 2.6491 0.9642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6491 -0.9642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 -5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7500 -6.4952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5000 -7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 -7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7500 -9.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2500 -9.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0000 -7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1491 -6.8300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1491 -8.7584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2500 -6.4952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0000 -5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2500 -3.8971 0.0000 C 0 0 0 0 0 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0 14 44 1 0 44 45 1 0 45 46 1 0 46 47 1 0 47 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 49 52 1 0 48 53 1 0 53 54 1 0 54 55 1 0 55 56 1 0 56 57 1 0 57 58 1 0 58 59 1 0 57 60 1 0 56 61 1 0 55 62 1 0 47 63 1 0 46 64 1 0 64 65 1 0 65 66 1 0 66 67 1 0 67 68 1 0 68 69 1 0 69 70 1 0 68 71 1 0 67 72 1 0 72 73 1 0 73 74 1 0 74 75 1 0 75 76 1 0 76 77 1 0 77 78 1 0 78 79 1 0 77 80 1 0 76 81 1 0 75 82 1 0 74 83 1 0 83 84 1 0 84 85 1 0 85 86 1 0 86 87 1 0 87 88 1 0 88 89 1 0 89 90 1 0 88 91 1 0 87 92 1 0 86 93 1 0 85 94 1 0 66 95 1 0 29 2 1 0 40 35 1 0 52 45 1 0 59 54 1 0 70 65 1 0 80 73 1 0 91 84 1 0 27 5 1 0 23 6 1 0 21 9 1 0 18 10 1 0 1 96 1 0 1 97 1 0 1 98 1 0 3 99 1 0 3100 1 0 3101 1 0 4102 1 0 4103 1 0 5104 1 6 7105 1 0 8106 1 0 8107 1 0 9108 1 1 11109 1 0 11110 1 0 11111 1 0 12112 1 0 12113 1 0 13114 1 0 13115 1 0 14116 1 1 16117 1 0 16118 1 0 16119 1 0 17120 1 0 17121 1 0 17122 1 0 18123 1 1 19124 1 0 19125 1 0 20126 1 0 20127 1 0 22128 1 0 22129 1 0 22130 1 0 24131 1 0 24132 1 0 24133 1 0 25134 1 0 25135 1 0 26136 1 0 26137 1 0 28138 1 0 28139 1 0 29140 1 1 33141 1 0 34142 1 0 36143 1 0 37144 1 0 38145 1 0 39146 1 0 40147 1 0 43148 1 0 45149 1 6 46150 1 1 47151 1 6 48152 1 1 49153 1 6 50154 1 0 50155 1 0 51156 1 0 54157 1 6 55158 1 1 56159 1 6 57160 1 1 58161 1 0 58162 1 0 60163 1 0 61164 1 0 62165 1 0 63166 1 0 65167 1 1 66168 1 6 67169 1 1 68170 1 6 69171 1 0 69172 1 0 71173 1 0 73174 1 6 74175 1 1 75176 1 6 76177 1 1 77178 1 6 78179 1 0 78180 1 0 79181 1 0 81182 1 0 82183 1 0 84184 1 1 85185 1 6 86186 1 1 87187 1 6 88188 1 1 89189 1 0 89190 1 0 90191 1 0 92192 1 0 93193 1 0 94194 1 0 95195 1 0 M END

Standard InCHIKey	HPWHBQBEUIHTFN-GQPKTZSISA-N
Standard InCHI	InChI=1S/C67H100O28/c1-62(2)23-32-31-14-15-39-64(5)19-18-40(63(3,4)38(64)17-20-66(39,7)65(31,6)21-22-67(32,61(83)84)24-41(62)90-42(73)16-13-30-11-9-8-10-12-30)91-59-55(50(81)53(37(27-70)89-59)93-56-48(79)43(74)33(71)28-85-56)94-57-51(82)52(34(72)29-86-57)92-60-54(47(78)45(76)36(26-69)88-60)95-58-49(80)46(77)44(75)35(25-68)87-58/h8-14,16,32-41,43-60,68-72,74-82H,15,17-29H2,1-7H3,(H,83,84)/b16-13+/t32-,33+,34+,35+,36+,37+,38-,39+,40-,41-,43-,44+,45+,46-,47-,48+,49+,50-,51+,52-,53+,54+,55+,56-,57-,58-,59-,60-,64-,65+,66+,67+/m0/s1
SMILES	CC1(C)C[C@H]2C3=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]4(C)[C@]3(C)CC[C@]2(C[C@@H]1OC(=O)/C=C/c1ccccc1)C(=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)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](CO)O1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1352.64	Volume:	1300.938 ? Van der Waals volume.
Dense:	1.04	LogP:	1.033 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.07 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.812 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	18.0	Rigid Bonds:	65.0
TPSA:	439.12 ? Topological Polar Surface Area.	H-Bond Acceptor:	28.0
H-Bond Donor:	15.0	Rings:	11.0
Heavy Atoms:	28.0

MedChem Properties

QED Drug-Likeness Score:	0.038	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.534	Fsp³:	0.821
MCE-18:	310.23 ? 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:	0.933	Fluc inhibitor:	0.314 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.062 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.095 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.289	Promiscuous compounds:	0.021

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.933	MDCK Permeability:	-5.164
Pgp-inhibitor:	0.0	Pgp-substrate:	0.355
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):	0.371
20% Bioavailability (F20%):	0.068	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.038
Plasma Protein Binding (PPB):	70.999%	Volume Distribution (VD):	-0.513
Fu:	19.608% ? 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:	0.157
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):

-0.825

Half-life (T1/2):

4.029

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.827	Drug-induced Liver Injury (DILI):	0.993
AMES Toxicity:	0.96	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.001	Skin Sensitization:	1.0
Carcinogencity:	0.011	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.636	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	0.18	RPMI-8226 Immunitoxicity:	0.162
A549 Cytotoxicity:	0.64	Hek293 Cytotoxicity:	0.208
BCF:	0.399 ? 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:	3.437 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.257 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.08 ? 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
NPO5418	Pachyelasma tessmannii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15686409]
NPO5418	Pachyelasma tessmannii	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
-	Biomphalaria glabrata	LD50	=	2.0	ug ml-1	PMID[19928832]

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 NPC264270 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	18155
0.1-0.2	27394
0.2-0.3	3137
0.3-0.4	733
0.4-0.5	380
0.5-0.6	49
0.6-0.7	1
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.938	High Similarity	NPC40085
0.8217	Intermediate Similarity	NPC111466
0.7794	Intermediate Similarity	NPC488210
0.7164	Intermediate Similarity	NPC488211
0.7	Intermediate Similarity	NPC488212
0.6031	Remote Similarity	NPC488561
0.5896	Remote Similarity	NPC114304
0.5874	Remote Similarity	NPC166422
0.5817	Remote Similarity	NPC120667
0.5817	Remote Similarity	NPC278272
0.5764	Remote Similarity	NPC251263
0.5743	Remote Similarity	NPC475513
0.5725	Remote Similarity	NPC79718
0.5649	Remote Similarity	NPC164194
0.5643	Remote Similarity	NPC324875
0.5643	Remote Similarity	NPC292677
0.5603	Remote Similarity	NPC488209
0.56	Remote Similarity	NPC471385
0.5586	Remote Similarity	NPC471384
0.5578	Remote Similarity	NPC54636
0.5536	Remote Similarity	NPC482013
0.553	Remote Similarity	NPC488215
0.5522	Remote Similarity	NPC25605
0.5481	Remote Similarity	NPC127056
0.5479	Remote Similarity	NPC323341
0.5474	Remote Similarity	NPC469945
0.5442	Remote Similarity	NPC219180
0.5429	Remote Similarity	NPC481082
0.5429	Remote Similarity	NPC164419
0.5374	Remote Similarity	NPC133818
0.535	Remote Similarity	NPC69425
0.5319	Remote Similarity	NPC257468
0.5294	Remote Similarity	NPC161717
0.5278	Remote Similarity	NPC488564
0.526	Remote Similarity	NPC329657
0.5245	Remote Similarity	NPC276093
0.5229	Remote Similarity	NPC470876
0.5221	Remote Similarity	NPC488214
0.52	Remote Similarity	NPC475140
0.5188	Remote Similarity	NPC33012
0.5177	Remote Similarity	NPC180550
0.5177	Remote Similarity	NPC35405
0.5145	Remote Similarity	NPC109079
0.5138	Remote Similarity	NPC476113
0.5125	Remote Similarity	NPC8524
0.5109	Remote Similarity	NPC12288
0.5108	Remote Similarity	NPC472949
0.5072	Remote Similarity	NPC56713
0.5072	Remote Similarity	NPC59804
0.507	Remote Similarity	NPC104400
0.507	Remote Similarity	NPC10320
0.5068	Remote Similarity	NPC288205
0.5068	Remote Similarity	NPC51465
0.5034	Remote Similarity	NPC475486
0.5034	Remote Similarity	NPC473824

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC264270 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4925
0.1-0.2	4176
0.2-0.3	45
0.3-0.4	4
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