NPASS Compound

Natural Product: NPC283806

Natural Product ID	NPC283806
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DXMITXYQZDSXOV-AXCBIKAISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	101682248
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] 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 72 75 0 0 0 0 0 0 0 0999 V2000 -1.2137 -4.5620 -2.9718 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4864 -4.0094 -1.9265 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5317 -2.6165 -1.9313 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9091 -2.1482 -2.1280 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2132 -1.2310 -0.9730 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1561 -0.1493 -0.9867 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1494 -0.8379 -0.5790 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3060 -0.2286 -1.2960 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5355 -0.7217 -0.8743 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9980 -0.6117 0.4075 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3516 -0.0571 1.3034 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3083 -1.1680 0.7465 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0975 -1.8039 -0.1902 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3249 -2.3248 0.1282 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8232 -2.2327 1.4086 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0536 -1.6023 2.3610 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8273 -1.0849 2.0315 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5525 -1.5039 3.6662 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.0787 -2.7664 1.7308 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.0958 -2.9551 -0.8214 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0638 -2.2105 -0.7313 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4555 0.9318 -0.1483 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5694 2.2397 -0.5735 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3899 2.4605 -1.7979 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8842 3.3427 0.3373 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9802 4.6201 -0.1672 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2718 5.7148 0.6168 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4799 5.5413 1.9708 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3839 4.2616 2.4773 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0892 3.1694 1.6733 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5858 4.0396 3.8360 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7783 6.6198 2.8078 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3675 7.0034 0.1004 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5144 -0.7636 -0.9285 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3937 -1.0440 0.1246 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9480 -1.7496 1.0456 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7565 -0.5380 0.1428 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5682 -0.8534 1.2120 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8840 -0.3864 1.2667 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3564 0.3873 0.2464 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5451 0.7080 -0.8316 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2508 0.2421 -0.8743 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0303 1.4954 -1.8671 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6653 0.8965 0.2242 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7195 -0.6852 2.3227 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7949 -3.1912 -2.2434 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8682 -4.2624 -3.9688 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3278 -5.6552 -2.8312 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2594 -4.1451 -2.8779 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1587 -2.3061 -2.7991 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9302 -1.4974 -3.0507 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0412 -1.8409 -0.0387 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0150 0.1475 -2.0504 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2539 -0.6312 0.5037 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2068 -0.2942 -2.4046 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2841 0.8758 -1.0769 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7345 -1.8943 -1.2117 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2087 -0.5864 2.7655 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3071 -2.0816 3.9739 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.7928 -2.7488 1.0044 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7470 -3.5193 -1.5682 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8228 4.8033 -1.2352 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0121 2.1625 2.0629 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5744 4.8338 4.4878 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7152 7.5591 2.4743 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9226 7.2786 -0.7604 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2416 -1.4620 2.0435 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6428 0.5034 -1.7181 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2611 2.4730 -1.7797 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3885 0.3252 0.6748 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0439 -1.6233 2.5382 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3941 -4.0507 -2.5047 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 15 19 1 0 14 20 1 0 7 21 1 0 6 22 1 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 29 31 1 0 28 32 1 0 27 33 1 0 5 34 1 0 34 35 1 0 35 36 2 0 35 37 1 0 37 38 2 0 38 39 1 0 39 40 2 0 40 41 1 0 41 42 2 0 41 43 1 0 40 44 1 0 39 45 1 0 4 46 1 0 21 3 1 0 30 25 1 0 42 37 1 0 17 12 1 0 1 47 1 0 1 48 1 0 1 49 1 0 3 50 1 6 4 51 1 6 5 52 1 1 6 53 1 6 7 54 1 1 8 55 1 0 8 56 1 0 13 57 1 0 17 58 1 0 18 59 1 0 19 60 1 0 20 61 1 0 26 62 1 0 30 63 1 0 31 64 1 0 32 65 1 0 33 66 1 0 38 67 1 0 42 68 1 0 43 69 1 0 44 70 1 0 45 71 1 0 46 72 1 0 M END

Standard InCHIKey	DXMITXYQZDSXOV-AXCBIKAISA-N
Standard InCHI	InChI=1S/C28H26O18/c1-42-28-22(38)24(46-27(41)11-6-16(33)21(37)17(34)7-11)23(45-26(40)10-4-14(31)20(36)15(32)5-10)18(44-28)8-43-25(39)9-2-12(29)19(35)13(30)3-9/h2-7,18,22-24,28-38H,8H2,1H3/t18-,22-,23-,24-,28+/m1/s1
SMILES	CO[C@@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)c2cc(c(c(c2)O)O)O)O1)OC(=O)c1cc(c(c(c1)O)O)O)OC(=O)c1cc(c(c(c1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	650.11	Volume:	585.205 ? Van der Waals volume.
Dense:	1.111	LogP:	0.703 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.779 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.668 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	Rigid Bonds:	27.0
TPSA:	299.66 ? Topological Polar Surface Area.	H-Bond Acceptor:	18.0
H-Bond Donor:	10.0	Rings:	4.0
Heavy Atoms:	18.0

MedChem Properties

QED Drug-Likeness Score:	0.089	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.381	Fsp³:	0.25
MCE-18:	105.143 ? 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:	0.896	Fluc inhibitor:	0.144 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.277 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.611 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.519	Promiscuous compounds:	0.981

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.789	MDCK Permeability:	-5.04
Pgp-inhibitor:	0.0	Pgp-substrate:	0.0
PAMPA:	0.998 ? 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):	0.0
20% Bioavailability (F20%):	0.994	30% Bioavailability (F30%):	0.989
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	61.31%	Volume Distribution (VD):	-0.135
Fu:	28.503% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.795
OATP1B3 inhibitor:	0.964	BCRP inhibitor:	0.863
BSEP inhibitor:	0.026

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.017
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.998
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.576 ? 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):

6.152

Half-life (T1/2):

2.926

ADMET: Toxicity

hERG Blockers:	0.024	hERG Blockers (10um):	0.986
Human Hepatotoxicity (H-HT):	0.014	Drug-induced Liver Injury (DILI):	0.979
AMES Toxicity:	0.819	Rat Oral Acute Toxicity:	0.046
Maximum Recommended Daily Dose:	0.759	Skin Sensitization:	1.0
Carcinogencity:	0.114	Eye Corrosion:	0.0
Eye Irritation:	0.953	Respiratory Toxicity:	0.027
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.999
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.0
Genotoxicity:	0.999	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.254
BCF:	0.417 ? 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:	3.371 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.434 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.239 ? 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
GI	3

Activity Type	# Activity
Cell line	3

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
NPT116	Cell line	HL-60	Homo sapiens	GI	=	64.2	%	PMID[32731188]
NPT165	Cell line	HeLa	Homo sapiens	GI	=	64.2	%	PMID[32731188]
NPT111	Cell line	K562	Homo sapiens	GI	=	64.2	%	PMID[32731188]

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 NPC283806 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	16921
0.1-0.2	31103
0.2-0.3	1612
0.3-0.4	137
0.4-0.5	59
0.5-0.6	20
0.6-0.7	3
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
0.88	High Similarity	NPC238419
0.7167	Intermediate Similarity	NPC302170
0.6607	Remote Similarity	NPC205037
0.6607	Remote Similarity	NPC3746
0.625	Remote Similarity	NPC16024
0.5965	Remote Similarity	NPC114791
0.5965	Remote Similarity	NPC104222
0.5965	Remote Similarity	NPC210501
0.5965	Remote Similarity	NPC318826
0.5965	Remote Similarity	NPC141331
0.5862	Remote Similarity	NPC61152
0.5862	Remote Similarity	NPC125546
0.5857	Remote Similarity	NPC470271
0.5789	Remote Similarity	NPC142528
0.5741	Remote Similarity	NPC610546
0.5667	Remote Similarity	NPC172419
0.5517	Remote Similarity	NPC239019
0.5517	Remote Similarity	NPC247629
0.5385	Remote Similarity	NPC488888
0.5303	Remote Similarity	NPC291957
0.5195	Remote Similarity	NPC481310
0.5167	Remote Similarity	NPC44260
0.5167	Remote Similarity	NPC92117
0.5147	Remote Similarity	NPC198125
0.5088	Remote Similarity	NPC226738

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC283806 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5020
0.1-0.2	4093
0.2-0.3	35
0.3-0.4	1
0.4-0.5	1
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