Natural Product: NPC485246

Natural Product IDNPC485246
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
UIHWDNARDUBWAO-MOPAQVBSSA-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

Standard InCHIKey UIHWDNARDUBWAO-MOPAQVBSSA-N
Standard InCHI InChI=1S/C136H220N38O38S6/c1-14-71(10)107-131(208)165-93-63-215-217-65-95-127(204)171-109(73(12)176)132(209)166-94(64-216-218-66-96(167-133(210)108(72(11)175)170-119(196)83(41-42-105(186)187)152-102(183)58-148-113(93)190)126(203)158-86(51-68(4)5)120(197)157-85(50-67(2)3)111(188)145-56-100(181)151-80(27-16-20-44-138)116(193)163-91(61-213)124(201)160-89(54-76-35-39-78(179)40-36-76)123(200)172-110(74(13)177)135(212)174-49-24-31-97(174)128(205)149-60-104(185)154-95)114(191)147-57-101(182)150-79(26-15-19-43-137)115(192)155-82(30-23-47-144-136(142)143)118(195)168-106(70(8)9)130(207)162-87(52-69(6)7)121(198)164-92(62-214)125(202)159-88(53-75-33-37-77(178)38-34-75)122(199)156-81(28-17-21-45-139)117(194)161-90(55-99(141)180)112(189)146-59-103(184)153-84(29-18-22-46-140)134(211)173-48-25-32-98(173)129(206)169-107/h33-40,67-74,79-98,106-110,175-179,213-214H,14-32,41-66,137-140H2,1-13H3,(H2,141,180)(H,145,188)(H,146,189)(H,147,191)(H,148,190)(H,149,205)(H,150,182)(H,151,181)(H,152,183)(H,153,184)(H,154,185)(H,155,192)(H,156,199)(H,157,197)(H,158,203)(H,159,202)(H,160,201)(H,161,194)(H,162,207)(H,163,193)(H,164,198)(H,165,208)(H,166,209)(H,167,210)(H,168,195)(H,169,206)(H,170,196)(H,171,204)(H,172,200)(H,186,187)(H4,142,143,144)/t71-,72+,73+,74+,79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,89-,90-,91-,92-,93-,94-,95-,96-,97-,98-,106-,107-,108-,109-,110-/m0/s1
SMILES CC[C@H](C)[C@H]1C(=N[C@H]2CSSC[C@H]3C(=N[C@@H]([C@@H](C)O)C(=N[C@@H](CSSC[C@@H](C(=N[C@@H](CC(C)C)C(=N[C@@H](CC(C)C)C(=NCC(=N[C@@H](CCCCN)C(=N[C@@H](CS)C(=N[C@@H](Cc4ccc(cc4)O)C(=N[C@@H]([C@@H](C)O)C(=O)N4CCC[C@H]4C(=NCC(=N3)O)O)O)O)O)O)O)O)O)N=C([C@H]([C@@H](C)O)N=C([C@H](CCC(=O)O)N=C(CN=C2O)O)O)O)C(=NCC(=N[C@@H](CCCCN)C(=N[C@@H](CCCNC(=N)N)C(=N[C@@H](C(C)C)C(=N[C@@H](CC(C)C)C(=N[C@@H](CS)C(=N[C@@H](Cc2ccc(cc2)O)C(=N[C@@H](CCCCN)C(=N[C@@H](CC(=N)O)C(=NCC(=N[C@@H](CCCCN)C(=O)N2CCC[C@H]2C(=N1)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   3185.48 Volume:   3061.053
?
Van der Waals volume.
Dense:   1.041 LogP:   -6.802
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -3.002
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -6.269
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   44.0 Rigid Bonds:   125.0
TPSA:   1301.65
?
Topological Polar Surface Area.
H-Bond Acceptor:   76.0
H-Bond Donor:   48.0 Rings:   7.0
Heavy Atoms:   82.0

MedChem Properties

QED Drug-Likeness Score:   0.01 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.9 Fsp3:   0.669
MCE-18:   311.775
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.333 Fluc inhibitor:   0.342
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.3
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.661
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.88 Promiscuous compounds:   0.165

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.158 MDCK Permeability:   -5.758
Pgp-inhibitor:   0.0 Pgp-substrate:   1.0
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):   1.0
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.807
Plasma Protein Binding (PPB):   -15.063% Volume Distribution (VD):   -0.793
Fu: 165.406%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.015 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.979 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
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):  -4.73 Half-life (T1/2):  10.678

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  1.0 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.0 Rat Oral Acute Toxicity:  0.626
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.96 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.089
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.921 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.443
?
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:   3.191
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.728
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.273
?
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
NPO40327 Rinorea bengalensis Species Violaceae Eukaryota n.a. n.a. n.a. PMID[30387611]
NPO40328 Rinorea virgata Species Violaceae Eukaryota n.a. n.a. n.a. PMID[30387611]
NPO40327 Rinorea bengalensis Species Violaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40328 Rinorea virgata Species Violaceae 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

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
NPT737 Cell line HUVEC Homo sapiens IC50 = 2800.0 nM PMID[30387611]
NPT1524 Cell line MM96L Homo sapiens IC50 = 930.0 nM PMID[30387611]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 = 4400.0 nM PMID[30387611]
NPT25044 Cell line HFF-1 Homo sapiens IC50 = 1700.0 nM PMID[30387611]

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
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 NPC485246 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9648 High Similarity NPC485245
0.9315 High Similarity NPC485243
0.8716 High Similarity NPC486507
0.8658 High Similarity NPC486505
0.8411 Intermediate Similarity NPC477632
0.8105 Intermediate Similarity NPC485115
0.7898 Intermediate Similarity NPC484365
0.7848 Intermediate Similarity NPC484964
0.7643 Intermediate Similarity NPC484963
0.755 Intermediate Similarity NPC485114
0.7547 Intermediate Similarity NPC484078
0.716 Intermediate Similarity NPC486515
0.7107 Intermediate Similarity NPC481408
0.7105 Intermediate Similarity NPC485116
0.7056 Intermediate Similarity NPC479083
0.6978 Remote Similarity NPC479082
0.6977 Remote Similarity NPC486506
0.6977 Remote Similarity NPC485247
0.6977 Remote Similarity NPC486514
0.6964 Remote Similarity NPC485125
0.6959 Remote Similarity NPC477635
0.689 Remote Similarity NPC484364
0.6875 Remote Similarity NPC485244
0.6848 Remote Similarity NPC482981
0.6824 Remote Similarity NPC486503
0.6758 Remote Similarity NPC486517
0.6726 Remote Similarity NPC486508
0.6647 Remote Similarity NPC489217
0.6629 Remote Similarity NPC329855
0.6622 Remote Similarity NPC485124
0.6536 Remote Similarity NPC489216
0.6484 Remote Similarity NPC329843
0.6465 Remote Similarity NPC480595
0.6461 Remote Similarity NPC329847
0.6364 Remote Similarity NPC484362
0.6343 Remote Similarity NPC484363
0.6319 Remote Similarity NPC489215
0.6303 Remote Similarity NPC485113
0.6162 Remote Similarity NPC477634
0.6145 Remote Similarity NPC329295
0.6118 Remote Similarity NPC486513
0.6108 Remote Similarity NPC477633
0.6021 Remote Similarity NPC489512
0.5924 Remote Similarity NPC480440
0.5907 Remote Similarity NPC486504
0.5882 Remote Similarity NPC481409
0.5742 Remote Similarity NPC489549
0.573 Remote Similarity NPC484965
0.5631 Remote Similarity NPC480594
0.5617 Remote Similarity NPC484875
0.5545 Remote Similarity NPC480596
0.5479 Remote Similarity NPC489511
0.5434 Remote Similarity NPC485242
0.5419 Remote Similarity NPC320968
0.5291 Remote Similarity NPC479131
0.5231 Remote Similarity NPC479128
0.5205 Remote Similarity NPC482856
0.516 Remote Similarity NPC479141
0.5125 Remote Similarity NPC484877
0.5064 Remote Similarity NPC479144
0.5056 Remote Similarity NPC482857
0.5033 Remote Similarity NPC296968
0.5027 Remote Similarity NPC479121

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC485246 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  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