NPASS Compound

Natural Product: NPC471091

Natural Product ID	NPC471091
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PAURBGYTYAPASF-UTIVGCTBSA-N
IUPAC Name	n.a.
Synonyms	Sanguiin H-6
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2368573
PubChem CID	73354402
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

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

Chemical Representations

RDKit 3D 188203 0 0 0 0 0 0 0 0999 V2000 -7.5681 1.2919 -3.2356 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9243 0.5963 -2.0314 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2845 -0.8996 -2.1353 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0674 -1.5376 -0.8276 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8393 -0.8529 -0.1257 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9504 -0.2468 -1.2421 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5679 0.7292 -1.9454 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7819 0.0816 -0.4968 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5438 -0.4405 -0.7189 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3655 -1.2023 -1.6909 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4283 -0.1401 0.1693 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5772 0.6241 1.3013 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5176 0.7374 2.2125 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6657 0.0793 1.9608 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8589 -0.6993 0.8294 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2136 -0.7727 -0.0311 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0633 -1.3038 0.6787 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6046 -1.9376 -0.4081 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0445 -3.0573 -0.9334 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6357 -3.6360 -2.0245 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7683 -3.0766 -2.5496 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3774 -1.9315 -2.0265 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7936 -1.3524 -0.9537 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1747 -0.1592 -0.2280 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1761 0.6469 0.0404 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3596 0.2751 0.2325 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5042 1.4961 0.9871 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6015 2.7449 0.2556 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1854 2.6873 -1.2306 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5577 1.5158 -1.7850 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4885 0.9027 -2.9731 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9466 1.4581 -3.9159 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0825 -0.4487 -3.1516 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3146 -0.3298 -3.8103 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1371 -1.4066 -3.9449 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7241 -2.5967 -3.4175 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5229 -2.6853 -2.7827 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6436 -1.5897 -2.6343 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1107 -3.9179 -2.2227 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5203 -3.7348 -3.5218 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3819 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21 82 1 0 20 83 1 0 19 84 1 0 14 85 1 0 13 86 1 0 5 87 1 0 87 88 1 0 88 89 2 0 88 90 1 0 90 91 2 0 91 92 1 0 92 93 2 0 93 94 1 0 94 95 2 0 95 96 1 0 96 97 2 0 97 98 1 0 98 99 2 0 99100 1 0 100101 2 0 101102 1 0 102103 2 0 102104 1 0 99105 1 0 98106 1 0 97107 1 0 93108 1 0 92109 1 0 91110 1 0 3111 1 0 111112 1 0 112113 2 0 112114 1 0 114115 2 0 115116 1 0 116117 2 0 117118 1 0 118119 2 0 119120 1 0 120121 2 0 121122 1 0 122123 2 0 123124 1 0 124125 2 0 125126 1 0 126127 2 0 126128 1 0 123129 1 0 122130 1 0 121131 1 0 118132 1 0 117133 1 0 116134 1 0 128 1 1 0 7 2 1 0 54 49 1 0 60 55 1 0 78 73 1 0 95 90 1 0 101 96 1 0 119114 1 0 125120 1 0 104 4 1 0 16 11 1 0 23 18 1 0 38 22 1 0 45 27 1 0 38 33 1 0 63 44 1 0 1135 1 0 1136 1 0 2137 1 0 3138 1 0 4139 1 0 5140 1 0 6141 1 0 12142 1 0 16143 1 0 27144 1 0 28145 1 0 29146 1 0 29147 1 0 34148 1 0 39149 1 0 40150 1 0 41151 1 0 43152 1 0 44153 1 0 45154 1 0 50155 1 0 59156 1 0 64157 1 0 65158 1 0 66159 1 0 67160 1 0 68161 1 0 69162 1 0 74163 1 0 78164 1 0 79165 1 0 80166 1 0 81167 1 0 82168 1 0 83169 1 0 84170 1 0 85171 1 0 86172 1 0 94173 1 0 100174 1 0 105175 1 0 106176 1 0 107177 1 0 108178 1 0 109179 1 0 110180 1 0 115181 1 0 124182 1 0 129183 1 0 130184 1 0 131185 1 0 132186 1 0 133187 1 0 134188 1 0 M END

Standard InCHIKey	PAURBGYTYAPASF-UTIVGCTBSA-N
Standard InCHI	InChI=1S/C82H54O52/c83-23-1-14(2-24(84)45(23)93)71(112)133-81-69-68(130-77(118)21-10-31(91)50(98)57(105)39(21)40-22(78(119)131-69)11-32(92)51(99)58(40)106)65-35(126-81)13-123-74(115)19-8-29(89)52(100)59(107)41(19)43-44(80(121)128-65)66(63(111)62(110)61(43)109)124-33-4-15(3-25(85)46(33)94)72(113)134-82-70-67(129-75(116)17-6-27(87)47(95)54(102)36(17)16-5-26(86)53(101)60(108)42(16)79(120)132-70)64-34(125-82)12-122-73(114)18-7-28(88)48(96)55(103)37(18)38-20(76(117)127-64)9-30(90)49(97)56(38)104/h1-11,34-35,64-65,67-70,81-111H,12-13H2/t34-,35-,64-,65-,67+,68+,69-,70-,81+,82+/m1/s1
SMILES	C1C2C(C3C(C(O2)OC(=O)C4=CC(=C(C(=C4)OC5=C(C(=C(C6=C5C(=O)OC7C(COC(=O)C8=CC(=C(C(=C86)O)O)O)OC(C9C7OC(=O)C2=CC(=C(C(=C2C2=C(C(=C(C=C2C(=O)O9)O)O)O)O)O)O)OC(=O)C2=CC(=C(C(=C2)O)O)O)O)O)O)O)O)OC(=O)C2=C(C(=C(C=C2C2=C(C(=C(C=C2C(=O)O3)O)O)O)O)O)O)OC(=O)C2=CC(=C(C(=C2C2=C(C(=C(C=C2C(=O)O1)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1870.16	Volume:	1641.557 ? Van der Waals volume.
Dense:	1.139	LogP:	-2.278 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-4.182 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.353 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	112.0
TPSA:	877.36 ? Topological Polar Surface Area.	H-Bond Acceptor:	52.0
H-Bond Donor:	29.0	Rings:	16.0
Heavy Atoms:	52.0

MedChem Properties

QED Drug-Likeness Score:	0.064	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.314	Fsp³:	0.146
MCE-18:	380.872 ? 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:	1	PAINS Alert:	1
Colloidal aggregators:	1.0	Fluc inhibitor:	0.009 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.027 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.667 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.81	Promiscuous compounds:	0.641

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-8.249	MDCK Permeability:	-5.266
Pgp-inhibitor:	0.0	Pgp-substrate:	0.0
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):	0.001
20% Bioavailability (F20%):	0.851	30% Bioavailability (F30%):	0.97
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	80.143%	Volume Distribution (VD):	-0.094
Fu:	9.28% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.0
OATP1B3 inhibitor:	0.124	BCRP inhibitor:	0.023
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.032
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.048 ? 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):

0.767

Half-life (T1/2):

10.985

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.999
Human Hepatotoxicity (H-HT):	0.183	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	0.999	Rat Oral Acute Toxicity:	0.004
Maximum Recommended Daily Dose:	0.998	Skin Sensitization:	1.0
Carcinogencity:	0.052	Eye Corrosion:	0.0
Eye Irritation:	0.332	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.022
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.318
BCF:	-1.737 ? 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:	2.789 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.62 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.24 ? 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
NPO26919	Sanguisorba officinalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520216]
NPO26919	Sanguisorba officinalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO26919	Sanguisorba officinalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26919	Sanguisorba officinalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26919	Sanguisorba officinalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26919	Sanguisorba officinalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26919	Sanguisorba officinalis	Species	Rosaceae	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
IC50	1
ED50	5

Activity Type	# Activity
Individual protein	1
Cell line	4
Non-molecular	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT326	Individual protein	Squalene monooxygenase	Rattus norvegicus	IC50	=	12000.0	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT672	Cell line	TE-671	Homo sapiens	ED50	>	10.0	ug ml-1	PubChem BioAssay data set
NPT180	Cell line	HCT-8	Homo sapiens	ED50	>	10.0	ug ml-1	Open TG-GATES in vivo data: Biochemistry
NPT81	Cell line	A549	Homo sapiens	ED50	>	10.0	ug ml-1	PMID[22512909]
NPT91	Cell line	KB	Homo sapiens	ED50	>	10.0	ug ml-1	DOI[10.6019/CHEMBL1201861]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	ED50	=	5.0	ug ml-1	PMID[1431932]

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 NPC471091 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	30119
0.1-0.2	19405
0.2-0.3	222
0.3-0.4	50
0.4-0.5	23
0.5-0.6	3
0.6-0.7	23
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.878	High Similarity	NPC97924
0.75	Intermediate Similarity	NPC223534
0.7363	Intermediate Similarity	NPC187632
0.7363	Intermediate Similarity	NPC240200
0.7356	Intermediate Similarity	NPC40078
0.7174	Intermediate Similarity	NPC488885
0.7021	Intermediate Similarity	NPC194439
0.7021	Intermediate Similarity	NPC33724
0.6739	Remote Similarity	NPC483712
0.6739	Remote Similarity	NPC158214
0.6739	Remote Similarity	NPC214202
0.6735	Remote Similarity	NPC488884
0.6667	Remote Similarity	NPC488887
0.6667	Remote Similarity	NPC290289
0.6667	Remote Similarity	NPC488886
0.6569	Remote Similarity	NPC469652
0.6569	Remote Similarity	NPC486025
0.6569	Remote Similarity	NPC486024
0.6442	Remote Similarity	NPC93065
0.6442	Remote Similarity	NPC220876
0.6346	Remote Similarity	NPC260521
0.6341	Remote Similarity	NPC47521
0.6265	Remote Similarity	NPC43918
0.6265	Remote Similarity	NPC261411
0.6265	Remote Similarity	NPC190204
0.619	Remote Similarity	NPC469651
0.617	Remote Similarity	NPC112211
0.617	Remote Similarity	NPC254925
0.6168	Remote Similarity	NPC31208
0.6168	Remote Similarity	NPC160543
0.6	Remote Similarity	NPC174140
0.581	Remote Similarity	NPC469649
0.5728	Remote Similarity	NPC116108
0.5385	Remote Similarity	NPC189312

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC471091 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6566
0.1-0.2	2580
0.2-0.3	4
0.3-0.4	0
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