NPASS Compound

Natural Product: NPC481489

Natural Product ID	NPC481489
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ONQOPPKTYBRABR-QVZZMKIVSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10417236
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002967] Hexacarboxylic acids and derivatives

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 95 98 0 0 0 0 0 0 0 0999 V2000 10.1443 -0.0855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6443 -0.0855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1443 -0.0855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1443 -1.5855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6443 -0.0855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0582 -1.4663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8943 1.2135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6443 2.5126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8943 3.8116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 3.8116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3557 2.5126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5048 1.5484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2760 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8943 -1.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6443 -0.0855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7934 0.8787 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2029 0.3656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0982 -1.1307 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3520 1.3298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7615 0.8168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9106 1.7810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6501 3.2582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2406 3.7712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0915 2.8070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3038 -1.8976 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5643 -3.3748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4152 -4.3390 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9738 -3.8878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3442 -2.2172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5241 -0.5932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3907 1.0037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8173 0.5402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1291 -0.9271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9320 1.5439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5048 3.4767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6338 5.2888 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7829 6.2530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1924 5.7400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5224 7.7302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7934 3.4767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2029 2.9637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1265 1.7818 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3520 3.9279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.6443 -0.0855 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1443 -1.5855 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3271 1.4033 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0073 1.3699 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8271 -1.5743 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5073 1.3699 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1443 -3.0855 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6331 -1.7684 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6555 -1.7684 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9320 2.6139 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9320 -0.1868 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1116 2.2009 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3038 4.3246 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0152 4.3246 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6548 5.2888 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7628 0.7315 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6018 2.5714 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8473 0.2002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6004 -0.7041 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8578 -2.6401 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8158 -2.8825 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5259 -1.2991 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0220 -0.6604 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3721 1.4436 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7992 4.2224 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1621 5.2692 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0879 3.9219 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3834 -4.4009 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4608 -5.2974 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3112 -2.4263 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6560 -3.6844 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8384 -2.0865 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0741 -2.7056 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0159 -0.4364 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8615 -2.0548 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5503 0.9066 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7707 2.7875 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3416 1.0310 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3946 2.9443 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9663 3.1394 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2619 9.2074 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9996 7.9907 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0452 7.4697 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3749 5.0250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3162 2.7788 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3878 5.0770 0.0000 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 3 5 1 0 5 6 2 0 5 7 1 0 7 8 1 0 9 8 1 6 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 18 29 1 0 29 30 1 0 30 31 2 0 30 32 1 0 17 33 1 0 33 34 1 0 33 35 1 0 33 36 1 0 16 37 1 0 37 38 1 0 38 39 2 0 38 40 1 0 13 41 1 1 11 42 1 0 42 43 1 0 43 44 2 0 43 45 1 0 10 46 1 0 46 47 1 0 47 48 2 0 47 49 1 0 19 9 1 0 28 23 1 0 15 9 1 0 15 36 1 1 1 50 1 0 1 51 1 0 1 52 1 0 2 53 1 0 2 54 1 0 3 55 1 0 4 56 1 0 4 57 1 0 4 58 1 0 8 59 1 0 8 60 1 0 10 61 1 1 11 62 1 1 12 63 1 0 12 64 1 0 14 65 1 0 14 66 1 0 14 67 1 0 16 68 1 1 17 69 1 6 18 70 1 6 19 71 1 1 24 72 1 0 25 73 1 0 26 74 1 0 27 75 1 0 28 76 1 0 32 77 1 0 32 78 1 0 32 79 1 0 34 80 1 0 34 81 1 0 34 82 1 0 35 83 1 0 35 84 1 0 35 85 1 0 40 86 1 0 40 87 1 0 40 88 1 0 41 89 1 0 45 90 1 0 45 91 1 0 45 92 1 0 49 93 1 0 49 94 1 0 49 95 1 0 M END

Standard InCHIKey	ONQOPPKTYBRABR-QVZZMKIVSA-N
Standard InCHI	InChI=1S/C35H46O14/c1-10-18(2)30(40)43-17-34-27(46-21(5)38)24(44-19(3)36)16-33(9,42)35(34)28(47-22(6)39)25(32(7,8)49-35)26(45-20(4)37)29(34)48-31(41)23-14-12-11-13-15-23/h11-15,18,24-29,42H,10,16-17H2,1-9H3/t18?,24-,25+,26-,27-,28+,29+,33-,34-,35-/m0/s1
SMILES	CCC(C)C(=O)OC[C@]12[C@H]([C@H](C[C@@](C)([C@]32[C@@H]([C@@H]([C@@H]([C@H]1OC(=O)c1ccccc1)OC(=O)C)C(C)(C)O3)OC(=O)C)O)OC(=O)C)OC(=O)C

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
NPO17696	Crossopetalum tonduzii	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[12932121]
NPO17696	Crossopetalum tonduzii	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17696	Crossopetalum tonduzii	Species	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
Activity	8

Activity Type	# Activity
Cell line	4
Others	4

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
NPT80	Cell line	Raji	Homo sapiens	Activity	=	70.0	%	PMID[12932121]
NPT80	Cell line	Raji	Homo sapiens	Activity	>	80.0	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	0.0	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	22.0	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	79.2	%	PMID[12932121]
NPT2	Others	Unspecified	n.a.	Activity	=	96.7	%	PMID[12932121]

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 NPC481489 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	13652
0.1-0.2	33878
0.2-0.3	1678
0.3-0.4	445
0.4-0.5	132
0.5-0.6	43
0.6-0.7	15
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9552	High Similarity	NPC481488
0.9242	High Similarity	NPC16912
0.8676	High Similarity	NPC472569
0.8676	High Similarity	NPC11685
0.8676	High Similarity	NPC472570
0.7703	Intermediate Similarity	NPC481486
0.72	Intermediate Similarity	NPC481490
0.7067	Intermediate Similarity	NPC97667
0.6944	Remote Similarity	NPC281717
0.6944	Remote Similarity	NPC483886
0.6933	Remote Similarity	NPC57628
0.6923	Remote Similarity	NPC488917
0.6892	Remote Similarity	NPC471104
0.6883	Remote Similarity	NPC479042
0.6842	Remote Similarity	NPC95265
0.6623	Remote Similarity	NPC70716
0.6538	Remote Similarity	NPC282239
0.6375	Remote Similarity	NPC481487
0.6329	Remote Similarity	NPC472568
0.6282	Remote Similarity	NPC479043
0.6265	Remote Similarity	NPC610134
0.6125	Remote Similarity	NPC471102
0.6053	Remote Similarity	NPC473060
0.5974	Remote Similarity	NPC147880
0.5909	Remote Similarity	NPC294512
0.5897	Remote Similarity	NPC472572
0.5843	Remote Similarity	NPC483868
0.5802	Remote Similarity	NPC106895
0.5696	Remote Similarity	NPC147217
0.5696	Remote Similarity	NPC148062
0.5618	Remote Similarity	NPC30171
0.557	Remote Similarity	NPC163719
0.557	Remote Similarity	NPC90257
0.557	Remote Similarity	NPC200471
0.557	Remote Similarity	NPC95810
0.557	Remote Similarity	NPC69357
0.557	Remote Similarity	NPC472575
0.5556	Remote Similarity	NPC176413
0.5556	Remote Similarity	NPC483885
0.5556	Remote Similarity	NPC479045
0.55	Remote Similarity	NPC137718
0.5455	Remote Similarity	NPC481047
0.5455	Remote Similarity	NPC481045
0.5443	Remote Similarity	NPC51314
0.5443	Remote Similarity	NPC472577
0.5432	Remote Similarity	NPC171207
0.5366	Remote Similarity	NPC479044
0.5309	Remote Similarity	NPC471101
0.5301	Remote Similarity	NPC252314
0.5238	Remote Similarity	NPC96903
0.5227	Remote Similarity	NPC125106
0.5227	Remote Similarity	NPC472573
0.5208	Remote Similarity	NPC6981
0.5185	Remote Similarity	NPC483845
0.5185	Remote Similarity	NPC479047
0.5185	Remote Similarity	NPC291638
0.5181	Remote Similarity	NPC483844
0.5125	Remote Similarity	NPC90614
0.5116	Remote Similarity	NPC294803
0.5116	Remote Similarity	NPC481062
0.5116	Remote Similarity	NPC481058
0.5116	Remote Similarity	NPC481060
0.5062	Remote Similarity	NPC483902
0.506	Remote Similarity	NPC473088
0.5056	Remote Similarity	NPC479048
0.5056	Remote Similarity	NPC610927

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC481489 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3830
0.1-0.2	5175
0.2-0.3	145
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