NPASS Compound

Natural Product: NPC602537

Natural Product ID	NPC602537
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	AMNQXXJPHNXOHG-QJLVSEQISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL486416
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001737] Flavonoid C-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 57 60 0 0 0 0 0 0 0 0999 V2000 9.7006 0.6896 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7908 -0.3745 0.1653 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4196 -0.1368 0.1030 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9055 1.1172 -0.1275 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5331 1.3443 -0.1879 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6274 0.3200 -0.0191 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1854 0.5180 -0.0754 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5904 1.7337 -0.3004 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1977 1.8653 -0.3443 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6376 2.9727 -0.5495 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4243 0.7397 -0.1553 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9547 0.7476 -0.1770 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5998 1.9566 -0.4015 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7017 -0.3801 0.0127 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1755 -0.4153 -0.0013 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7004 0.4928 -0.9462 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0618 0.1757 -1.0310 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6699 0.6602 -2.3231 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0167 0.2952 -2.3045 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7288 0.8202 0.1578 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0435 0.3467 0.3336 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9204 0.7290 1.4028 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.5102 2.0113 1.8350 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7702 -0.2004 1.3588 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0993 -1.4429 1.9256 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0349 -1.5898 0.2377 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7643 -2.7544 0.4342 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0653 -3.9578 0.6586 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3423 -1.6029 0.2603 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0902 -0.4601 0.0679 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3965 -0.5136 0.0966 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1607 -0.9496 0.2144 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5178 -1.1629 0.2722 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6463 1.4030 0.8607 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5017 1.2192 -0.9660 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7254 0.2612 -0.1009 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6181 1.9277 -0.2611 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1958 2.3626 -0.3739 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2027 2.5997 -0.4455 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6810 2.6649 0.3233 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4892 -1.4156 -0.3617 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2120 -0.9184 -0.9675 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2081 0.0922 -3.1617 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5771 1.7522 -2.4535 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0815 -0.6930 -2.4053 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8498 1.9104 -0.1121 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6942 0.9107 -0.1220 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6134 0.3753 2.2223 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8981 2.4352 1.2129 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9599 0.2155 2.0088 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8748 -1.3088 2.5273 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4757 -4.2797 -0.2163 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3426 -3.8562 1.5189 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8089 -4.7685 0.8708 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8437 -2.5632 0.4385 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4275 -1.7570 0.3472 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9022 -2.1637 0.4557 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 17 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 22 24 1 0 24 25 1 0 14 26 2 0 26 27 1 0 27 28 1 0 26 29 1 0 29 30 2 0 30 31 1 0 6 32 1 0 32 33 2 0 33 3 1 0 31 7 1 0 30 11 1 0 24 15 1 0 1 34 1 0 1 35 1 0 1 36 1 0 4 37 1 0 5 38 1 0 8 39 1 0 13 40 1 0 15 41 1 6 17 42 1 1 18 43 1 0 18 44 1 0 19 45 1 0 20 46 1 6 21 47 1 0 22 48 1 1 23 49 1 0 24 50 1 1 25 51 1 0 28 52 1 0 28 53 1 0 28 54 1 0 29 55 1 0 32 56 1 0 33 57 1 0 M END

Standard InCHIKey	AMNQXXJPHNXOHG-QJLVSEQISA-N
Standard InCHI	InChI=1S/C23H24O10/c1-30-11-5-3-10(4-6-11)13-7-12(25)17-15(32-13)8-14(31-2)18(20(17)27)23-22(29)21(28)19(26)16(9-24)33-23/h3-8,16,19,21-24,26-29H,9H2,1-2H3/t16-,19-,21+,22-,23+/m1/s1
SMILES	COc1ccc(-c2cc(=O)c3c(O)c([C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)c(OC)cc3o2)cc1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	460.14	Volume:	438.949 ? Van der Waals volume.
Dense:	1.048	LogP:	1.313 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.864 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.355 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	24.0
TPSA:	159.05 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	5.0	Rings:	4.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.367	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.835	Fsp³:	0.348
MCE-18:	86.387 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.539	Fluc inhibitor:	0.323 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.788 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.802 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.076	Promiscuous compounds:	0.27

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.88	MDCK Permeability:	-5.189
Pgp-inhibitor:	0.0	Pgp-substrate:	0.199
PAMPA:	0.992 ? 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):	0.958
20% Bioavailability (F20%):	0.393	30% Bioavailability (F30%):	0.962
50% Bioavailability (F50%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.694
Plasma Protein Binding (PPB):	90.364%	Volume Distribution (VD):	-0.009
Fu:	10.025% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.795
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.093
BSEP inhibitor:	0.311

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.617	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.002	CYP2D6-substrate:	0.065
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.999
HLM stability:	0.1 ? 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):

4.277

Half-life (T1/2):

3.821

ADMET: Toxicity

hERG Blockers:	0.036	hERG Blockers (10um):	0.122
Human Hepatotoxicity (H-HT):	0.53	Drug-induced Liver Injury (DILI):	0.963
AMES Toxicity:	0.846	Rat Oral Acute Toxicity:	0.062
Maximum Recommended Daily Dose:	0.145	Skin Sensitization:	0.912
Carcinogencity:	0.528	Eye Corrosion:	0.0
Eye Irritation:	0.568	Respiratory Toxicity:	0.078
Drug-induced Neurotoxicity:	0.011	Ototoxicity:	0.761
Hematotoxicity:	0.317	Drug-induced Nephrotoxicity:	0.397
Genotoxicity:	0.729	RPMI-8226 Immunitoxicity:	0.115
A549 Cytotoxicity:	0.256	Hek293 Cytotoxicity:	0.371
BCF:	0.368 ? 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:	3.196 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.717 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.843 ? 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
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075762]
NPO7478	Iris germanica	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO7478	Iris germanica	Species	Iridaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[22388969]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24433009]
NPO7478	Iris germanica	Species	Iridaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[25204177]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28032759]
NPO54610	Siphonoglossa canbyi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25831	Siphonoglossa sessilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16515	Siphonoglossa mexicana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7478	Iris germanica	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7478	Iris germanica	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7478	Iris germanica	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7478	Iris germanica	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14417	Iris tectorum	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25831	Siphonoglossa sessilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO16515	Siphonoglossa mexicana	n.a.	n.a.	n.a.	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
Inhibition	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1310	Individual protein	Xanthine dehydrogenase	Bos taurus	Inhibition	=	33.5	%	PMID[3379415]

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

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 NPC602537 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	20124
0.1-0.2	25889
0.2-0.3	3048
0.3-0.4	604
0.4-0.5	162
0.5-0.6	19
0.6-0.7	7
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8592	High Similarity	NPC10807
0.8592	High Similarity	NPC161881
0.7024	Intermediate Similarity	NPC606373
0.6824	Remote Similarity	NPC257566
0.6709	Remote Similarity	NPC304745
0.6706	Remote Similarity	NPC607513
0.6279	Remote Similarity	NPC603300
0.619	Remote Similarity	NPC111249
0.6	Remote Similarity	NPC328740
0.6	Remote Similarity	NPC289774
0.5783	Remote Similarity	NPC95090
0.5783	Remote Similarity	NPC27408
0.5732	Remote Similarity	NPC53545
0.5732	Remote Similarity	NPC220912
0.5714	Remote Similarity	NPC186807
0.5663	Remote Similarity	NPC58053
0.5357	Remote Similarity	NPC112701
0.5342	Remote Similarity	NPC145379
0.5301	Remote Similarity	NPC209846
0.5205	Remote Similarity	NPC29353
0.5169	Remote Similarity	NPC243930
0.5169	Remote Similarity	NPC80188
0.5135	Remote Similarity	NPC18260
0.5135	Remote Similarity	NPC57030
0.5111	Remote Similarity	NPC607707
0.5067	Remote Similarity	NPC78913
0.5059	Remote Similarity	NPC117418
0.5056	Remote Similarity	NPC609451
0.5052	Remote Similarity	NPC150767

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602537 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4406
0.1-0.2	4631
0.2-0.3	96
0.3-0.4	16
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