NPASS Compound

Natural Product: NPC130886

Natural Product ID	NPC130886
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DQYTUBPKRGEWBN-JBMBANNUSA-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 3D 93 99 0 0 0 0 0 0 0 0999 V2000 9.9386 1.1443 2.3086 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3606 0.5375 0.9817 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8207 1.2609 -0.2057 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3516 1.2717 -0.3280 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5440 0.6679 0.5120 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0942 0.7685 0.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1911 0.2065 1.0295 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7735 0.3362 0.7371 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8220 -0.2008 1.4610 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3708 -0.0451 1.1264 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5780 0.0350 2.2391 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6276 0.4862 1.6730 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2070 -0.7151 0.9473 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4065 -1.8466 1.9208 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1394 -2.9712 1.6351 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8727 -3.7185 2.7656 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2258 -3.6418 2.4773 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4996 -3.4428 0.3042 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0138 -2.6914 -0.8673 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5523 -2.3444 -0.8543 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0817 -2.4738 -2.2340 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9359 -3.2189 -2.9007 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8528 -3.6154 -4.3545 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0306 -3.6415 -2.0395 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7912 -4.6009 -2.2783 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2621 -1.0227 -0.1906 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3104 0.0830 -1.2085 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0273 0.3217 -1.8586 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7716 1.4253 -0.6192 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1372 1.5384 0.7015 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1367 2.8134 1.3982 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7601 3.8818 1.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6691 2.8848 2.6552 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2172 1.1711 0.5302 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1832 1.5008 -0.6697 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8765 2.3409 -1.5288 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1501 3.0507 -2.2846 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3295 2.4412 -1.5997 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1753 1.7543 -0.8720 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6242 1.8652 -0.9532 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4319 1.0780 -0.1445 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8069 1.1287 -0.1616 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4429 1.9959 -1.0149 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6687 2.7910 -1.8309 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2859 2.7205 -1.7944 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0283 -1.1159 0.3169 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8482 -1.6559 -1.2387 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9157 -3.4433 0.2304 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6739 -3.0051 1.8660 O 0 0 0 0 0 0 0 0 0 0 0 0 10.8281 1.6788 2.7739 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1814 1.9377 2.1614 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6153 0.3332 2.9711 H 0 0 0 0 0 0 0 0 0 0 0 0 11.4754 0.4931 0.9831 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0318 -0.5262 0.9178 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2373 0.7211 -1.1090 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2560 2.2845 -0.2850 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9057 1.8252 -1.1862 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9354 0.1172 1.3361 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7170 1.3334 -0.6014 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5000 -0.3559 1.8847 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4277 0.9134 -0.1355 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0732 -0.7804 2.3328 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3268 0.8764 2.4242 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2190 -0.4166 0.6191 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4823 -1.4470 2.9852 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5810 -4.7844 2.7637 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6936 -3.2277 3.7351 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6060 -2.7454 2.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2126 -4.5202 0.1995 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0420 -3.1939 -0.3086 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7993 -2.0531 -2.6502 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8640 -3.7104 -4.7939 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3789 -2.7321 -4.8529 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1974 -4.4810 -4.5086 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0515 -0.1334 -2.0181 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8483 -0.2911 -1.4698 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9409 0.2778 -2.9901 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3949 1.3880 -1.7215 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3737 2.1862 -1.3163 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6770 4.7938 1.6324 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3602 4.0215 0.1254 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6631 2.4150 2.5483 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0791 2.2671 3.3954 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6920 3.8964 3.0748 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7410 3.1329 -2.3074 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7448 1.0575 -0.1620 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9356 0.3914 0.5317 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3622 0.4668 0.5154 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.5268 2.0123 -1.0016 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2022 3.4717 -2.5001 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7276 3.3629 -2.4510 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7640 -2.0310 -1.2754 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2907 -4.3157 0.0393 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 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 10 9 1 1 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 1 16 17 1 0 15 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 22 24 1 0 24 25 2 0 20 26 1 0 26 27 1 0 27 28 1 0 27 29 1 0 29 30 1 0 30 31 1 1 31 32 2 0 31 33 1 0 30 34 1 0 29 35 1 0 35 36 1 0 36 37 2 0 36 38 1 0 38 39 2 0 39 40 1 0 40 41 2 0 41 42 1 0 42 43 2 0 43 44 1 0 44 45 2 0 26 46 1 1 19 47 1 6 18 48 1 0 15 49 1 0 34 10 1 0 45 40 1 0 46 10 1 0 30 12 1 0 26 13 1 0 49 14 1 0 24 19 1 0 1 50 1 0 1 51 1 0 1 52 1 0 2 53 1 0 2 54 1 0 3 55 1 0 3 56 1 0 4 57 1 0 5 58 1 0 6 59 1 0 7 60 1 0 8 61 1 0 9 62 1 0 12 63 1 1 13 64 1 6 14 65 1 1 16 66 1 0 16 67 1 0 17 68 1 0 18 69 1 6 20 70 1 1 21 71 1 0 23 72 1 0 23 73 1 0 23 74 1 0 27 75 1 6 28 76 1 0 28 77 1 0 28 78 1 0 29 79 1 6 32 80 1 0 32 81 1 0 33 82 1 0 33 83 1 0 33 84 1 0 38 85 1 0 39 86 1 0 41 87 1 0 42 88 1 0 43 89 1 0 44 90 1 0 45 91 1 0 47 92 1 0 48 93 1 0 M END

Standard InCHIKey	DQYTUBPKRGEWBN-JBMBANNUSA-N
Standard InCHI	InChI=1S/C39H44O10/c1-6-7-8-9-10-11-15-20-36-47-33-29-32-35(22-40,46-32)34(43)37(44)27(21-24(4)30(37)42)39(29,49-36)25(5)31(38(33,48-36)23(2)3)45-28(41)19-18-26-16-13-12-14-17-26/h8-21,25,27,29,31-34,40,43-44H,2,6-7,22H2,1,3-5H3/b9-8+,11-10+,19-18+,20-15+/t25-,27-,29+,31-,32+,33-,34-,35+,36-,37-,38+,39+/m1/s1
SMILES	CCC/C=C/C=C/C=C/[C@@]12O[C@@H]3[C@@H]4[C@H]5[C@@](CO)([C@H]([C@]6([C@@H](C=C(C)C6=O)[C@]4([C@H](C)[C@H]([C@]3(C(=C)C)O1)OC(=O)/C=C/c1ccccc1)O2)O)O)O5

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32997496]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4035	Daphne odora	Species	Thymelaeaceae	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
EC50	1
IC50	1

Activity Type	# Activity
Cell line	1
Organism	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
NPT25	Cell line	MT4	Homo sapiens	IC50	>	34.0	nM	PMID[32997496]
NPT1114	Organism	Human immunodeficiency virus	Human immunodeficiency virus	EC50	=	3.7	nM	PMID[32997496]

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 NPC130886 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	10686
0.1-0.2	36920
0.2-0.3	2095
0.3-0.4	92
0.4-0.5	12
0.5-0.6	17
0.6-0.7	8
0.7-0.8	0
0.8-0.85	2
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.931	High Similarity	NPC101786
0.8876	High Similarity	NPC481774
0.8652	High Similarity	NPC486153
0.828	Intermediate Similarity	NPC481773
0.8144	Intermediate Similarity	NPC191992
0.7765	Intermediate Similarity	NPC324104
0.7765	Intermediate Similarity	NPC473548
0.7717	Intermediate Similarity	NPC164150
0.7717	Intermediate Similarity	NPC481754
0.7624	Intermediate Similarity	NPC69240
0.7191	Intermediate Similarity	NPC223356
0.7191	Intermediate Similarity	NPC298697
0.7191	Intermediate Similarity	NPC475500
0.7191	Intermediate Similarity	NPC100017
0.7191	Intermediate Similarity	NPC481742
0.7188	Intermediate Similarity	NPC92598
0.7188	Intermediate Similarity	NPC43304
0.7188	Intermediate Similarity	NPC481753
0.7188	Intermediate Similarity	NPC477188
0.7188	Intermediate Similarity	NPC477190
0.7111	Intermediate Similarity	NPC182266
0.7111	Intermediate Similarity	NPC475154
0.7111	Intermediate Similarity	NPC485700
0.7111	Intermediate Similarity	NPC75831
0.7111	Intermediate Similarity	NPC471137
0.7033	Intermediate Similarity	NPC471136
0.7033	Intermediate Similarity	NPC116727
0.7033	Intermediate Similarity	NPC39509
0.6957	Remote Similarity	NPC481744
0.6957	Remote Similarity	NPC481743
0.6566	Remote Similarity	NPC486154
0.6522	Remote Similarity	NPC180902
0.6289	Remote Similarity	NPC275477
0.6196	Remote Similarity	NPC475606
0.6139	Remote Similarity	NPC156682
0.6139	Remote Similarity	NPC49297
0.5957	Remote Similarity	NPC251564
0.5957	Remote Similarity	NPC477189
0.5895	Remote Similarity	NPC474508
0.5895	Remote Similarity	NPC473485
0.5895	Remote Similarity	NPC171411
0.5895	Remote Similarity	NPC485701
0.5729	Remote Similarity	NPC475314
0.5729	Remote Similarity	NPC102997
0.567	Remote Similarity	NPC485693
0.5545	Remote Similarity	NPC605479
0.5472	Remote Similarity	NPC481745
0.5283	Remote Similarity	NPC481776
0.5258	Remote Similarity	NPC162495
0.5248	Remote Similarity	NPC481750
0.5152	Remote Similarity	NPC181924
0.505	Remote Similarity	NPC481751
0.5046	Remote Similarity	NPC68282

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC130886 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3961
0.1-0.2	5130
0.2-0.3	59
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