NPASS Compound

Natural Product: NPC256760

Natural Product ID	NPC256760
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Farobin B
IUPAC Name	6-[(2R,4S,5R,6R)-4,5-dihydroxy-6-methyloxan-2-yl]-5,7-dihydroxy-2-[3-hydroxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]chromen-4-one
Synonyms	farobin B
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1224896
PubChem CID	46938450
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides

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 71 75 0 0 0 0 0 0 0 0999 V2000 8.4649 -1.6569 -2.2493 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2165 -1.0660 -1.2302 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3452 -0.2293 -0.3518 C 0 0 1 0 0 0 0 0 0 0 0 0 7.3314 -0.9478 0.2613 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4274 -0.0193 0.7791 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2767 -0.5870 1.2852 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9733 -0.4233 0.9218 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5804 0.4071 -0.0945 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2242 0.5464 -0.4366 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2525 -0.1467 0.2388 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6921 -0.9860 1.2716 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0137 -1.1326 1.6176 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4118 -1.9845 2.6595 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1759 -0.0517 -0.0616 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6505 0.7555 -1.0620 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0209 0.8396 -1.3419 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4691 1.5699 -2.2495 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8792 0.0785 -0.5724 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3326 -0.7093 0.4150 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0234 -0.7435 0.6290 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1855 -1.4699 1.1846 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5496 -1.4412 0.9699 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1132 -0.6577 -0.0148 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2517 0.1004 -0.7804 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7883 0.8879 -1.7663 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5774 -0.6196 -0.2538 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2765 0.4386 0.5498 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4998 0.9414 -0.2217 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.3980 1.4914 0.6743 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.0808 -0.2085 -0.9861 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.0746 -0.7154 -1.9836 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7754 -0.3660 -1.6111 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3102 -0.1018 -3.3546 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2271 0.2363 -1.6678 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3647 -2.2424 1.7917 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0609 0.8227 1.8673 C 0 0 1 0 0 0 0 0 0 0 0 0 8.3881 1.3996 1.4549 C 0 0 2 0 0 0 0 0 0 0 0 0 9.2176 0.3284 0.7788 C 0 0 2 0 0 0 0 0 0 0 0 0 10.3850 0.8327 0.2487 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0232 1.8489 2.6114 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1977 1.9005 2.1117 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5503 -1.1728 -3.1061 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6521 -1.8713 -0.6141 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0054 -0.4092 -1.6494 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9429 0.6713 -0.8825 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1910 0.6694 -0.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3105 0.9738 -0.6553 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9417 1.2127 -1.2477 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9242 -1.5280 1.7986 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3384 -1.6582 3.6002 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0041 1.3586 -1.6751 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7847 -2.1143 1.9862 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8868 1.8859 -1.5902 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9662 -1.6489 -0.0105 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6474 -0.0245 1.4873 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6026 1.3071 0.7561 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1125 1.7255 -0.9192 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8969 1.8491 1.4503 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3315 -1.0059 -0.2524 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0891 -1.8394 -2.0528 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9431 -0.8063 -3.9130 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7767 0.8866 -3.1990 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3342 -0.0414 -3.8919 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.6511 -0.5502 -2.1187 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5426 -1.8355 2.7222 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2284 0.2076 2.7747 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2626 2.2238 0.7114 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3895 -0.5224 1.4872 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1527 0.3643 0.6759 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5867 1.4876 3.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6267 1.7441 2.9050 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 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 10 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 0 19 20 1 0 19 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 23 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 31 32 1 0 31 33 1 0 30 34 1 0 22 35 1 0 5 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 37 40 1 0 36 41 1 0 38 3 1 0 12 7 1 0 20 14 1 0 32 26 1 0 24 18 1 0 1 42 1 0 2 43 1 0 2 44 1 0 3 45 1 6 5 46 1 6 8 47 1 0 9 48 1 0 11 49 1 0 13 50 1 0 15 51 1 0 21 52 1 0 25 53 1 0 26 54 1 1 27 55 1 0 27 56 1 0 28 57 1 6 29 58 1 0 30 59 1 1 31 60 1 6 33 61 1 0 33 62 1 0 33 63 1 0 34 64 1 0 35 65 1 0 36 66 1 1 37 67 1 6 38 68 1 1 39 69 1 0 40 70 1 0 41 71 1 0 M END

Standard InCHIKey	NJNUVWMGNSDFQJ-GIZWKEFHSA-N
Standard InCHI	InChI=1S/C27H30O14/c1-9-22(33)14(32)7-17(38-9)20-13(31)6-18-21(24(20)35)12(30)5-16(39-18)10-2-3-15(11(29)4-10)40-27-26(37)25(36)23(34)19(8-28)41-27/h2-6,9,14,17,19,22-23,25-29,31-37H,7-8H2,1H3/t9-,14+,17-,19-,22+,23-,25+,26-,27-/m1/s1
SMILES	OC[C@H]1O[C@@H](Oc2ccc(cc2O)c2cc(=O)c3c(o2)cc(c(c3O)[C@H]2C[C@H](O)[C@H]([C@H](O2)C)O)O)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	578.16	Volume:	534.737 ? Van der Waals volume.
Dense:	1.081	LogP:	0.724 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.138 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.66 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	30.0
TPSA:	239.97 ? Topological Polar Surface Area.	H-Bond Acceptor:	14.0
H-Bond Donor:	9.0	Rings:	5.0
Heavy Atoms:	14.0

MedChem Properties

QED Drug-Likeness Score:	0.182	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.821	Fsp³:	0.444
MCE-18:	119.436 ? 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:	0
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.622	Fluc inhibitor:	0.18 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.962 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.596 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.206	Promiscuous compounds:	0.604

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.418	MDCK Permeability:	-5.162
Pgp-inhibitor:	0.0	Pgp-substrate:	0.922
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):	0.345
20% Bioavailability (F20%):	0.663	30% Bioavailability (F30%):	0.997
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.305
Plasma Protein Binding (PPB):	85.053%	Volume Distribution (VD):	-0.028
Fu:	12.206% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.158
BSEP inhibitor:	0.001

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.009	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.002
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.974
HLM stability:	0.063 ? 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):

2.314

Half-life (T1/2):

4.774

ADMET: Toxicity

hERG Blockers:	0.011	hERG Blockers (10um):	0.079
Human Hepatotoxicity (H-HT):	0.601	Drug-induced Liver Injury (DILI):	0.856
AMES Toxicity:	0.924	Rat Oral Acute Toxicity:	0.101
Maximum Recommended Daily Dose:	0.399	Skin Sensitization:	0.989
Carcinogencity:	0.11	Eye Corrosion:	0.0
Eye Irritation:	0.121	Respiratory Toxicity:	0.036
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.914
Hematotoxicity:	0.074	Drug-induced Nephrotoxicity:	0.229
Genotoxicity:	0.932	RPMI-8226 Immunitoxicity:	0.244
A549 Cytotoxicity:	0.66	Hek293 Cytotoxicity:	0.628
BCF:	0.381 ? 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:	2.914 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.613 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.621 ? 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
NPO33290	fargesia robusta	Species	Poaceae	Eukaryota	leaves	n.a.	n.a.	PMID[20863141]

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

Activity Type	# Activity
Others	1
Non-molecular	1

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
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	0.075	n.a.	PMID[20863141]
NPT35	Others	n.a.	n.a.	Activity	=	8.3	n.a.	PMID[20056520]

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 NPC256760 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	13763
0.1-0.2	31893
0.2-0.3	3197
0.3-0.4	796
0.4-0.5	163
0.5-0.6	35
0.6-0.7	6
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
0.6701	Remote Similarity	NPC150767
0.6667	Remote Similarity	NPC191306
0.6596	Remote Similarity	NPC603300
0.625	Remote Similarity	NPC611357
0.6237	Remote Similarity	NPC605067
0.604	Remote Similarity	NPC124155
0.5895	Remote Similarity	NPC22832
0.5684	Remote Similarity	NPC21100
0.5545	Remote Similarity	NPC78734
0.5532	Remote Similarity	NPC143851
0.5464	Remote Similarity	NPC60735
0.5464	Remote Similarity	NPC26230
0.5464	Remote Similarity	NPC285197
0.5417	Remote Similarity	NPC58716
0.5408	Remote Similarity	NPC486578
0.5408	Remote Similarity	NPC601710
0.5408	Remote Similarity	NPC609478
0.534	Remote Similarity	NPC218488
0.534	Remote Similarity	NPC607513
0.5263	Remote Similarity	NPC53545
0.5248	Remote Similarity	NPC294629
0.5248	Remote Similarity	NPC131407
0.5208	Remote Similarity	NPC58053
0.5208	Remote Similarity	NPC45618
0.52	Remote Similarity	NPC88023
0.52	Remote Similarity	NPC111249
0.52	Remote Similarity	NPC309025
0.5196	Remote Similarity	NPC251417
0.5196	Remote Similarity	NPC472607
0.5155	Remote Similarity	NPC95090
0.5155	Remote Similarity	NPC146792
0.5155	Remote Similarity	NPC27408
0.5155	Remote Similarity	NPC189142
0.5155	Remote Similarity	NPC77660
0.5102	Remote Similarity	NPC186807
0.5102	Remote Similarity	NPC45638
0.51	Remote Similarity	NPC120099
0.51	Remote Similarity	NPC601144
0.5096	Remote Similarity	NPC47923
0.5052	Remote Similarity	NPC254306
0.5051	Remote Similarity	NPC201292

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC256760 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4057
0.1-0.2	5002
0.2-0.3	75
0.3-0.4	14
0.4-0.5	2
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