NPASS Compound

Natural Product: NPC602979

Natural Product ID	NPC602979
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NLWUWPJUIJTHAN-UDLCBVDQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1929103
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan 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 64 69 0 0 0 0 0 0 0 0999 V2000 -1.0973 4.6038 -0.2368 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2914 4.2670 -0.1254 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6818 2.9406 -0.0056 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2402 1.9160 0.0102 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1050 0.5753 0.1277 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8268 -0.4387 0.1436 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1479 -0.1465 0.0390 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9354 -0.0309 -1.1186 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4967 1.2065 -1.1925 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5883 1.4207 -0.3547 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1823 1.1936 1.0676 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7495 0.5321 -0.7715 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1901 -0.1300 0.3676 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2553 -0.5163 -1.7548 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.2516 -1.5035 -1.8416 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9394 -1.1064 -1.3035 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5203 -2.1009 -2.1925 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3932 -1.7410 0.2666 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9424 -2.0414 0.3726 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8495 -0.9943 0.3521 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2794 -1.2834 0.4599 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0534 -1.5078 -0.6559 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3993 -1.7817 -0.5515 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9979 -1.8356 0.6840 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2291 -1.6107 1.8267 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8822 -1.3384 1.6903 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0595 -1.7204 2.9313 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1899 -2.4717 2.5373 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2924 -2.0773 1.1614 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4733 0.3260 0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4021 1.3479 0.2162 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0274 2.6661 0.0982 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9950 3.6364 0.0891 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3726 3.3109 0.1988 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1391 -3.4748 0.4999 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2160 -4.0930 0.6147 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1097 -4.0346 0.4691 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1146 -3.0550 0.3177 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4400 4.1942 -1.2252 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6263 4.1019 0.6021 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1993 5.7079 -0.1871 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2715 2.1972 -0.0701 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2032 -0.1171 -1.9806 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9113 2.4664 -0.4783 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8678 1.8221 1.7036 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2782 0.1286 1.3626 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1724 1.5850 1.2347 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5653 1.1290 -1.1833 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0342 -0.6215 0.2183 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1223 -0.0434 -2.7474 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0851 -1.0105 -2.0780 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1695 -1.6550 -0.3426 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2149 -2.8054 -2.2336 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6374 -1.4794 -1.6723 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0198 -1.9603 -1.4239 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3387 -1.1712 2.6369 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0557 -2.0996 3.1308 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0457 -3.5629 2.6351 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4523 1.0849 0.3007 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0007 4.2143 0.2984 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7125 2.6714 -0.6428 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4459 2.6663 1.1200 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5555 -3.2322 -0.6945 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8318 -3.1195 1.1343 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 1 0 8 9 1 0 9 10 1 0 10 11 1 0 10 12 1 0 12 13 1 0 12 14 1 0 14 15 1 0 14 16 1 0 16 17 1 0 6 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 25 27 1 0 27 28 1 0 28 29 1 0 20 30 2 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 1 0 19 35 1 0 35 36 2 0 35 37 1 0 37 38 1 0 32 3 1 0 30 5 1 0 16 8 1 0 38 18 1 0 26 21 1 0 29 24 1 0 1 39 1 0 1 40 1 0 1 41 1 0 4 42 1 0 8 43 1 6 10 44 1 1 11 45 1 0 11 46 1 0 11 47 1 0 12 48 1 6 13 49 1 0 14 50 1 6 15 51 1 0 16 52 1 1 17 53 1 0 22 54 1 0 23 55 1 0 26 56 1 0 28 57 1 0 28 58 1 0 31 59 1 0 34 60 1 0 34 61 1 0 34 62 1 0 38 63 1 0 38 64 1 0 M END

Standard InCHIKey	NLWUWPJUIJTHAN-UDLCBVDQSA-N
Standard InCHI	InChI=1S/C27H26O11/c1-11-22(28)23(29)24(30)27(37-11)38-25-14-8-18(33-3)17(32-2)7-13(14)20(21-15(25)9-34-26(21)31)12-4-5-16-19(6-12)36-10-35-16/h4-8,11,22-24,27-30H,9-10H2,1-3H3/t11-,22+,23+,24-,27+/m1/s1
SMILES	COc1cc2c(O[C@@H]3O[C@H](C)[C@H](O)[C@H](O)[C@H]3O)c3c(c(-c4ccc5c(c4)OCO5)c2cc1OC)C(=O)OC3

Calculated Properties

Physi-Chem Properties

Molecular Weight:	526.15	Volume:	497.174 ? Van der Waals volume.
Dense:	1.058	LogP:	2.272 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.417 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.273 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	32.0
TPSA:	142.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	11.0
H-Bond Donor:	3.0	Rings:	6.0
Heavy Atoms:	11.0

MedChem Properties

QED Drug-Likeness Score:	0.421	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.093	Fsp³:	0.37
MCE-18:	118.243 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.834	Fluc inhibitor:	0.066 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.702 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.761 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.036	Promiscuous compounds:	0.387

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.812	MDCK Permeability:	-4.999
Pgp-inhibitor:	0.004	Pgp-substrate:	0.231
PAMPA:	0.949 ? 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):	0.213
20% Bioavailability (F20%):	0.275	30% Bioavailability (F30%):	0.009
50% Bioavailability (F50%):	0.942

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.061	MRP1:	0.711
Plasma Protein Binding (PPB):	97.461%	Volume Distribution (VD):	-0.206
Fu:	3.19% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.998
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.14
BSEP inhibitor:	0.926

ADMET: Metabolism

CYP1A2-inhibitor:	0.794	CYP1A2-substrate:	0.006
CYP2C19-inhibitor:	0.668	CYP2C19-substrate:	0.006
CYP2C9-inhibitor:	0.071	CYP2C9-substrate:	0.022
CYP2D6-inhibitor:	0.002	CYP2D6-substrate:	0.906
CYP3A4-inhibitor:	0.008	CYP3A4-substrate:	0.991
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.848
HLM stability:	0.538 ? 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):

2.388

Half-life (T1/2):

2.834

ADMET: Toxicity

hERG Blockers:	0.114	hERG Blockers (10um):	0.532
Human Hepatotoxicity (H-HT):	0.934	Drug-induced Liver Injury (DILI):	0.996
AMES Toxicity:	0.976	Rat Oral Acute Toxicity:	0.293
Maximum Recommended Daily Dose:	0.675	Skin Sensitization:	1.0
Carcinogencity:	0.912	Eye Corrosion:	0.0
Eye Irritation:	0.026	Respiratory Toxicity:	0.138
Drug-induced Neurotoxicity:	0.621	Ototoxicity:	0.92
Hematotoxicity:	0.971	Drug-induced Nephrotoxicity:	0.986
Genotoxicity:	0.984	RPMI-8226 Immunitoxicity:	0.491
A549 Cytotoxicity:	0.908	Hek293 Cytotoxicity:	0.871
BCF:	1.162 ? 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:	3.806 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.61 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.741 ? 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
NPO20590	Justicia patentiflora	Species	Acanthaceae	Eukaryota	n.a.	Vietnamese	n.a.	PMID[15921419]
NPO20590	Justicia patentiflora	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20590	Justicia patentiflora	Species	Acanthaceae	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
Inhibition	1
Activity	9
IC50	3

Activity Type	# Activity
Individual protein	1
Cell line	12

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1044	Individual protein	DNA topoisomerase II alpha	Homo sapiens	Inhibition	n.a.	n.a.	%	PMID[22119124]

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	Activity	=	40.5	%	PMID[22119124]
NPT116	Cell line	HL-60	Homo sapiens	Activity	=	30.0	%	PMID[22119124]
NPT116	Cell line	HL-60	Homo sapiens	Activity	=	34.6	%	PMID[22119124]
NPT116	Cell line	HL-60	Homo sapiens	Activity	=	31.5	%	PMID[22119124]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	6430.0	nM	PMID[22119124]
NPT91	Cell line	KB	Homo sapiens	IC50	=	3050.0	nM	PMID[22119124]
NPT393	Cell line	HCT-116	Homo sapiens	Activity	n.a.	n.a.	n.a.	PMID[22119124]
NPT116	Cell line	HL-60	Homo sapiens	Activity	=	24.9	%	PMID[22119124]
NPT83	Cell line	MCF7	Homo sapiens	IC50	=	1810.0	nM	PMID[22119124]
NPT116	Cell line	HL-60	Homo sapiens	Activity	=	38.6	%	PMID[22119124]
NPT116	Cell line	HL-60	Homo sapiens	Activity	n.a.	n.a.	n.a.	PMID[22119124]

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 NPC602979 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	18529
0.1-0.2	29115
0.2-0.3	2082
0.3-0.4	89
0.4-0.5	12
0.5-0.6	7
0.6-0.7	14
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC114550
1.0	High Similarity	NPC312006
0.8571	High Similarity	NPC129930
0.7805	Intermediate Similarity	NPC292712
0.7722	Intermediate Similarity	NPC474075
0.7722	Intermediate Similarity	NPC483381
0.7381	Intermediate Similarity	NPC471922
0.7059	Intermediate Similarity	NPC471921
0.7024	Intermediate Similarity	NPC20114
0.6988	Remote Similarity	NPC184624
0.6944	Remote Similarity	NPC239113
0.6897	Remote Similarity	NPC471920
0.6712	Remote Similarity	NPC19600
0.6706	Remote Similarity	NPC473531
0.6596	Remote Similarity	NPC275690
0.6429	Remote Similarity	NPC161609
0.6383	Remote Similarity	NPC35266
0.6383	Remote Similarity	NPC167045
0.6383	Remote Similarity	NPC114120
0.6353	Remote Similarity	NPC474442
0.6292	Remote Similarity	NPC471923
0.6267	Remote Similarity	NPC115123
0.6	Remote Similarity	NPC473697
0.5769	Remote Similarity	NPC78944
0.557	Remote Similarity	NPC15212
0.5556	Remote Similarity	NPC286301
0.5556	Remote Similarity	NPC313063
0.5176	Remote Similarity	NPC196771
0.5122	Remote Similarity	NPC22130
0.5062	Remote Similarity	NPC299820

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602979 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4880
0.1-0.2	4228
0.2-0.3	41
0.3-0.4	1
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