NPASS Compound

Natural Product: NPC486024

Natural Product ID	NPC486024
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	CNUXVAAAAPNLJA-WWCJQXKLSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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

Chemical Representations

RDKit 2D 270290 0 0 0 0 0 0 0 0999 V2000 4.9300 13.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1800 12.6423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6800 12.6423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9300 13.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6800 15.2404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1800 15.2404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9300 16.5394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9300 16.5394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4300 13.9413 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9300 11.3433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4188 11.5261 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1800 10.0442 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9300 8.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0791 9.7094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4886 9.1963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9518 9.5268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0040 10.5958 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3112 12.0641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.8065 12.1829 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7759 13.4653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1500 14.0667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3163 15.5574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1084 16.4468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7342 15.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5680 14.3546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0710 14.4498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7602 13.7205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4732 14.4910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4970 15.9908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8078 16.7201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0948 15.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4055 16.6789 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8316 18.2199 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2100 16.7613 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0518 12.3983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7016 13.0516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1707 10.9030 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5263 16.7348 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.2746 17.9375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.6904 16.1588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7491 7.7191 0.0000 O 0 0 0 0 0 0 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0 0 0 0 0 -8.4481 11.0084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.6981 12.3074 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1981 14.9055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1981 14.9055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2990 7.4462 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0490 8.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1463 9.9431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5490 8.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2990 10.0442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7990 10.0442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5490 8.7452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7990 7.4462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2990 7.4462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5490 6.1471 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0490 6.1471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2990 4.8481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7990 4.8481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0490 6.1471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7990 7.4462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2990 7.4462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0490 8.7452 0.0000 O 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179262 1 0 180263 1 0 184264 1 0 185265 1 0 186266 1 0 187267 1 0 188268 1 0 189269 1 0 190270 1 0 M END

Standard InCHIKey	CNUXVAAAAPNLJA-WWCJQXKLSA-N
Standard InCHI	InChI=1S/C116H80O74/c117-37-1-23(2-38(118)65(37)133)100(156)183-94-91-56(20-171-105(161)28-11-45(125)70(138)79(147)59(28)62-31(108(164)180-91)14-48(128)73(141)82(62)150)177-114(170)97(94)186-111(167)34-17-51(131)76(144)85(153)88(34)174-53-9-26(7-43(123)68(53)136)103(159)189-115-98(95(184-101(157)24-3-39(119)66(134)40(120)4-24)92-57(178-115)21-172-106(162)29-12-46(126)71(139)80(148)60(29)63-32(109(165)181-92)15-49(129)74(142)83(63)151)187-112(168)35-18-52(132)77(145)86(154)89(35)176-55-19-36-90(87(155)78(55)146)175-54-10-27(8-44(124)69(54)137)104(160)190-116-99(188-113(36)169)96(185-102(158)25-5-41(121)67(135)42(122)6-25)93-58(179-116)22-173-107(163)30-13-47(127)72(140)81(149)61(30)64-33(110(166)182-93)16-50(130)75(143)84(64)152/h1-19,56-58,91-99,114-155,170H,20-22H2/t56-,57-,58-,91-,92-,93-,94+,95+,96+,97-,98-,99-,114?,115+,116+/m1/s1
SMILES	c1c(cc(c(c1O)O)O)C(=O)O[C@H]1[C@H]2[C@@H](COC(=O)c3cc(c(c(c3-c3c(cc(c(c3O)O)O)C(=O)O2)O)O)O)OC([C@@H]1OC(=O)c1cc(c(c(c1Oc1cc(cc(c1O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@H]2[C@@H](COC(=O)c3cc(c(c(c3-c3c(cc(c(c3O)O)O)C(=O)O2)O)O)O)O1)OC(=O)c1cc(c(c(c1)O)O)O)OC(=O)c1cc(c(c(c1Oc1cc2c(c(c1O)O)Oc1cc(cc(c1O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@H]3[C@@H](COC(=O)c4cc(c(c(c4-c4c(cc(c(c4O)O)O)C(=O)O3)O)O)O)O1)OC(=O)c1cc(c(c(c1)O)O)O)OC2=O)O)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	2656.25	Volume:	2338.04 ? Van der Waals volume.
Dense:	1.136	LogP:	-3.156 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-5.173 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.895 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	22.0	Rigid Bonds:	148.0
TPSA:	1232.78 ? Topological Polar Surface Area.	H-Bond Acceptor:	74.0
H-Bond Donor:	40.0	Rings:	21.0
Heavy Atoms:	74.0

MedChem Properties

QED Drug-Likeness Score:	0.033	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	9.309	Fsp³:	0.155
MCE-18:	513.179 ? 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:	0.087 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.356 ? 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:	0.635	Promiscuous compounds:	0.98

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-11.446	MDCK Permeability:	-4.51
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):	0.0
20% Bioavailability (F20%):	0.998	30% Bioavailability (F30%):	0.999
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	72.497%	Volume Distribution (VD):	0.034
Fu:	5.975% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.738
OATP1B3 inhibitor:	0.218	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.739
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.0 ? 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):

1.872

Half-life (T1/2):

15.098

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	1.0
Human Hepatotoxicity (H-HT):	0.179	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	1.0	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.996	Skin Sensitization:	1.0
Carcinogencity:	0.004	Eye Corrosion:	0.0
Eye Irritation:	0.007	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.003
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.741
BCF:	-2.47 ? 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:	2.825 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.471 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.249 ? 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
NPO18996	Tamarix aphylla	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31532650]
NPO18996	Tamarix aphylla	Species	Tamaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18996	Tamarix aphylla	Species	Tamaricaceae	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
CC50	6

Activity Type	# Activity
Cell line	3
Others	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
NPT1031	Cell line	Ca9-22	Homo sapiens	CC50	=	27000.0	nM	PMID[31532650]
NPT924	Cell line	HSC-2	Homo sapiens	CC50	=	23000.0	nM	PMID[31532650]
NPT2394	Cell line	HSC-4	Homo sapiens	CC50	=	26000.0	nM	PMID[31532650]
NPT2	Others	Unspecified	n.a.	CC50	>	75000.0	nM	PMID[31532650]

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 NPC486024 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	29249
0.1-0.2	20218
0.2-0.3	275
0.3-0.4	48
0.4-0.5	28
0.5-0.6	9
0.6-0.7	11
0.7-0.8	0
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC469652
1.0	High Similarity	NPC486025
0.954	High Similarity	NPC488887
0.954	High Similarity	NPC488886
0.8736	High Similarity	NPC187632
0.8736	High Similarity	NPC240200
0.8068	Intermediate Similarity	NPC223534
0.7912	Intermediate Similarity	NPC488885
0.7778	Intermediate Similarity	NPC93065
0.7778	Intermediate Similarity	NPC220876
0.7742	Intermediate Similarity	NPC194439
0.7742	Intermediate Similarity	NPC33724
0.7727	Intermediate Similarity	NPC40078
0.7423	Intermediate Similarity	NPC488884
0.7391	Intermediate Similarity	NPC290289
0.7283	Intermediate Similarity	NPC483712
0.7283	Intermediate Similarity	NPC158214
0.7283	Intermediate Similarity	NPC97924
0.7283	Intermediate Similarity	NPC214202
0.7157	Intermediate Similarity	NPC260521
0.6952	Remote Similarity	NPC31208
0.6952	Remote Similarity	NPC160543
0.6882	Remote Similarity	NPC112211
0.6882	Remote Similarity	NPC254925
0.6569	Remote Similarity	NPC471091
0.6455	Remote Similarity	NPC174140
0.6286	Remote Similarity	NPC469649
0.6092	Remote Similarity	NPC43918
0.6092	Remote Similarity	NPC261411
0.6092	Remote Similarity	NPC190204
0.6023	Remote Similarity	NPC469651
0.5977	Remote Similarity	NPC47521
0.5977	Remote Similarity	NPC175793
0.5977	Remote Similarity	NPC159913
0.5905	Remote Similarity	NPC469650
0.5755	Remote Similarity	NPC116108
0.566	Remote Similarity	NPC483711
0.5402	Remote Similarity	NPC31034
0.5243	Remote Similarity	NPC269625
0.5043	Remote Similarity	NPC486110

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC486024 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7034
0.1-0.2	2111
0.2-0.3	5
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