NPASS Compound

Natural Product: NPC123204

Natural Product ID	NPC123204
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Murucoidin X
IUPAC Name	n.a.
Synonyms	Murucoidin X
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL509954
PubChem CID	24899658
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

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 198203 0 0 0 0 0 0 0 0999 V2000 13.1689 8.4555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.9131 7.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.6574 6.8146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4016 5.9942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1459 5.1738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8901 4.3534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1459 3.5329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0672 2.3492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5543 0.9305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5543 -0.5695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0672 -1.9882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1459 -3.1719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8901 -3.9924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4360 -4.3606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9412 -4.2367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5675 -3.6342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7471 -4.8899 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4639 -2.6182 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4639 2.9793 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5675 3.9952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9412 4.5977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4360 4.7216 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1062 6.0886 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8975 6.9770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0656 8.2251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5239 6.3744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3589 4.8835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6939 3.5390 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0270 6.2780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 1.2990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6491 -0.9642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4895 -2.7762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6386 -3.7404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4895 -4.7046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -6.1818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4895 -7.6590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 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39 1 0 39 40 1 0 40 41 1 0 40 42 1 0 42 43 1 0 43 44 1 0 44 45 1 0 45 46 1 0 46 47 2 0 46 48 1 0 48 49 1 0 49 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 53 54 1 0 54 55 1 0 55 56 1 0 56 57 1 0 57 58 1 0 54 59 1 0 43 60 1 0 60 61 1 0 61 62 1 0 62 63 1 0 63 64 1 0 63 65 1 0 65 66 1 0 66 67 1 0 67 68 1 0 66 69 1 0 65 70 1 0 42 71 1 0 71 72 1 0 72 73 1 0 73 74 1 0 74 75 1 0 74 76 1 0 76 77 1 0 77 78 1 0 78 79 1 0 77 80 1 0 76 81 1 0 81 82 1 0 82 83 2 0 82 84 1 0 84 85 1 0 85 86 1 0 84 87 1 0 20 88 1 0 25 6 1 0 44 38 1 0 67 61 1 0 78 72 1 0 36 19 1 0 30 23 1 0 1 89 1 0 1 90 1 0 1 91 1 0 2 92 1 0 2 93 1 0 3 94 1 0 3 95 1 0 4 96 1 0 4 97 1 0 5 98 1 0 5 99 1 0 6100 1 6 7101 1 0 7102 1 0 8103 1 0 8104 1 0 9105 1 0 9106 1 0 10107 1 0 10108 1 0 11109 1 0 11110 1 0 12111 1 0 12112 1 0 13113 1 0 13114 1 0 14115 1 0 14116 1 0 15117 1 0 15118 1 0 19119 1 1 20120 1 1 21121 1 6 23122 1 1 24123 1 6 27124 1 6 28125 1 0 28126 1 0 28127 1 0 29128 1 6 30129 1 6 31130 1 0 32131 1 0 34132 1 1 35133 1 0 35134 1 0 35135 1 0 36136 1 6 38137 1 1 40138 1 6 41139 1 0 41140 1 0 41141 1 0 42142 1 1 43143 1 6 44144 1 6 48145 1 0 48146 1 0 49147 1 0 49148 1 0 50149 1 0 50150 1 0 51151 1 0 51152 1 0 52153 1 0 52154 1 0 53155 1 0 53156 1 0 54157 1 1 55158 1 0 55159 1 0 56160 1 0 56161 1 0 57162 1 0 57163 1 0 58164 1 0 58165 1 0 58166 1 0 59167 1 0 61168 1 6 63169 1 1 64170 1 0 64171 1 0 64172 1 0 65173 1 6 66174 1 1 67175 1 1 68176 1 0 69177 1 0 70178 1 0 72179 1 6 74180 1 1 75181 1 0 75182 1 0 75183 1 0 76184 1 6 77185 1 1 78186 1 1 79187 1 0 80188 1 0 84189 1 1 85190 1 0 85191 1 0 86192 1 0 86193 1 0 86194 1 0 87195 1 0 87196 1 0 87197 1 0 88198 1 0 M END

Standard InCHIKey	LGUWRLBGQNAXKS-USOWJTJTSA-N
Standard InCHI	InChI=1S/C63H110O25/c1-10-13-22-29-40-30-24-18-16-15-17-19-25-31-41(65)82-54-50(74)61(87-55-46(70)44(68)35(6)77-62(55)81-40)79-37(8)52(54)86-63-57(83-42(66)32-26-21-20-23-28-39(64)27-14-11-2)56(88-59-48(72)45(69)43(67)34(5)76-59)53(38(9)80-63)85-60-49(73)47(71)51(36(7)78-60)84-58(75)33(4)12-3/h33-40,43-57,59-64,67-74H,10-32H2,1-9H3/t33-,34-,35+,36-,37-,38-,39+,40-,43-,44-,45+,46-,47-,48+,49+,50+,51-,52-,53-,54-,55+,56+,57+,59-,60-,61-,62-,63-/m0/s1
SMILES	CCCCC[C@H]1CCCCCCCCCC(=O)O[C@H]2[C@H]([C@H](O[C@H]3[C@H](O1)O[C@H](C)[C@@H]([C@@H]3O)O)O[C@@H](C)[C@@H]2O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1OC(=O)CCCCCC[C@@H](CCCC)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)OC(=O)[C@H](CC)C)O

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
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	Roots	Ixpantepec, in the state of Oaxaca, Mexico	1996-DEC	PMID[16124750]
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	flowers	n.a.	n.a.	PMID[16643033]
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18500841]
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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
MIC	4
ED50	3

Activity Type	# Activity
Cell line	3
Organism	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
NPT1171	Cell line	HEp-2	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[18610999]
NPT165	Cell line	HeLa	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[23131541]
NPT91	Cell line	KB	Homo sapiens	ED50	=	15.7	ug ml-1	PMID[25028062]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	512.0	ug.mL-1	PMID[17190450]

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 NPC123204 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	23624
0.1-0.2	23302
0.2-0.3	2690
0.3-0.4	110
0.4-0.5	22
0.5-0.6	36
0.6-0.7	36
0.7-0.8	0
0.8-0.85	4
0.85-0.9	8
0.9-0.95	5
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9494	High Similarity	NPC307400
0.9494	High Similarity	NPC27289
0.925	High Similarity	NPC143421
0.9125	High Similarity	NPC477319
0.9024	High Similarity	NPC290012
0.8765	High Similarity	NPC267592
0.869	High Similarity	NPC183888
0.869	High Similarity	NPC259294
0.8608	High Similarity	NPC113745
0.8608	High Similarity	NPC477320
0.8608	High Similarity	NPC477323
0.8608	High Similarity	NPC477325
0.8608	High Similarity	NPC609436
0.8471	Intermediate Similarity	NPC126685
0.8118	Intermediate Similarity	NPC472204
0.8101	Intermediate Similarity	NPC146380
0.8023	Intermediate Similarity	NPC483170
0.7857	Intermediate Similarity	NPC477326
0.7701	Intermediate Similarity	NPC119583
0.7619	Intermediate Similarity	NPC604005
0.7619	Intermediate Similarity	NPC605014
0.7528	Intermediate Similarity	NPC115013
0.7273	Intermediate Similarity	NPC10121
0.7273	Intermediate Similarity	NPC198918
0.7262	Intermediate Similarity	NPC281563
0.7241	Intermediate Similarity	NPC477344
0.7216	Intermediate Similarity	NPC35338
0.7216	Intermediate Similarity	NPC204214
0.7216	Intermediate Similarity	NPC92283
0.7191	Intermediate Similarity	NPC472205
0.7143	Intermediate Similarity	NPC169345
0.7126	Intermediate Similarity	NPC478734
0.7126	Intermediate Similarity	NPC89843
0.7065	Intermediate Similarity	NPC184915
0.7065	Intermediate Similarity	NPC224953
0.7041	Intermediate Similarity	NPC63404
0.6966	Remote Similarity	NPC478733
0.6957	Remote Similarity	NPC477317
0.6957	Remote Similarity	NPC477318
0.6915	Remote Similarity	NPC44782
0.6897	Remote Similarity	NPC22742
0.6897	Remote Similarity	NPC477346
0.6867	Remote Similarity	NPC606819
0.6854	Remote Similarity	NPC600446
0.6854	Remote Similarity	NPC605013
0.6813	Remote Similarity	NPC297768
0.6768	Remote Similarity	NPC124878
0.6768	Remote Similarity	NPC231888
0.6703	Remote Similarity	NPC146992
0.6703	Remote Similarity	NPC85759
0.6667	Remote Similarity	NPC476087
0.6667	Remote Similarity	NPC475667
0.6596	Remote Similarity	NPC478732
0.6593	Remote Similarity	NPC109887
0.6559	Remote Similarity	NPC294748
0.6526	Remote Similarity	NPC475270
0.6526	Remote Similarity	NPC475327
0.6489	Remote Similarity	NPC238264
0.6489	Remote Similarity	NPC477345
0.6452	Remote Similarity	NPC173328
0.6442	Remote Similarity	NPC10883
0.6421	Remote Similarity	NPC238056
0.6322	Remote Similarity	NPC477350
0.6304	Remote Similarity	NPC158302
0.6289	Remote Similarity	NPC472200
0.6211	Remote Similarity	NPC186992
0.6174	Remote Similarity	NPC147032
0.6162	Remote Similarity	NPC475164
0.6139	Remote Similarity	NPC475241
0.6082	Remote Similarity	NPC478731
0.6042	Remote Similarity	NPC478730
0.6022	Remote Similarity	NPC477331
0.5946	Remote Similarity	NPC472352
0.5941	Remote Similarity	NPC473605
0.5941	Remote Similarity	NPC475375
0.59	Remote Similarity	NPC269318
0.5833	Remote Similarity	NPC290276
0.5806	Remote Similarity	NPC477349
0.5702	Remote Similarity	NPC471024
0.5644	Remote Similarity	NPC163409
0.5644	Remote Similarity	NPC475525
0.5644	Remote Similarity	NPC475540
0.5636	Remote Similarity	NPC600672
0.5625	Remote Similarity	NPC479059
0.5588	Remote Similarity	NPC476066
0.5556	Remote Similarity	NPC77651
0.5545	Remote Similarity	NPC611287
0.5536	Remote Similarity	NPC600721
0.5536	Remote Similarity	NPC605872
0.5455	Remote Similarity	NPC479058
0.5439	Remote Similarity	NPC600940
0.5426	Remote Similarity	NPC477329
0.5413	Remote Similarity	NPC28069
0.5385	Remote Similarity	NPC478729
0.5361	Remote Similarity	NPC477332
0.5354	Remote Similarity	NPC479061
0.5354	Remote Similarity	NPC60849
0.5347	Remote Similarity	NPC478726
0.5319	Remote Similarity	NPC477330
0.531	Remote Similarity	NPC471025
0.5304	Remote Similarity	NPC610997
0.53	Remote Similarity	NPC479060
0.5221	Remote Similarity	NPC610996
0.5189	Remote Similarity	NPC478727
0.5158	Remote Similarity	NPC477328
0.5146	Remote Similarity	NPC162925
0.5094	Remote Similarity	NPC478728
0.505	Remote Similarity	NPC478722

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC123204 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7620
0.1-0.2	1478
0.2-0.3	51
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