Natural Product: NPC485115

Natural Product IDNPC485115
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
BCYJBUHPQWOPTH-QJUFSFBYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 49799160
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0003297] Organic Polymers
      • [CHEMONTID:0003298] Polypeptides

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 BCYJBUHPQWOPTH-QJUFSFBYSA-N
Standard InCHI InChI=1S/C139H219N37O41S6/c1-17-71(14)108-136(215)162-88(58-179)121(200)160-89(59-180)124(203)170-105(68(8)9)132(211)157-81(48-66(4)5)111(190)146-54-100(184)150-91-61-219-218-60-90-113(192)148-53-99(183)149-80(41-42-102(186)187)116(195)159-86(56-177)122(201)164-94-64-222-220-62-92(163-123(202)87(57-178)161-125(91)204)126(205)153-77(32-23-25-43-140)114(193)155-84(51-98(142)182)119(198)151-78(33-24-26-44-141)117(196)169-107(70(12)13)134(213)167-93(63-221-223-65-95(129(208)172-108)166-131(210)97-36-29-46-175(97)137(216)109(72(15)18-2)173-120(199)83(49-74-30-21-20-22-31-74)158-133(212)106(69(10)11)171-128(94)207)127(206)154-82(50-75-37-39-76(181)40-38-75)118(197)152-79(34-27-45-145-139(143)144)115(194)156-85(52-103(188)189)112(191)147-55-101(185)168-104(67(6)7)135(214)174-110(73(16)19-3)138(217)176-47-28-35-96(176)130(209)165-90/h20-22,30-31,37-40,66-73,77-97,104-110,177-181H,17-19,23-29,32-36,41-65,140-141H2,1-16H3,(H2,142,182)(H,146,190)(H,147,191)(H,148,192)(H,149,183)(H,150,184)(H,151,198)(H,152,197)(H,153,205)(H,154,206)(H,155,193)(H,156,194)(H,157,211)(H,158,212)(H,159,195)(H,160,200)(H,161,204)(H,162,215)(H,163,202)(H,164,201)(H,165,209)(H,166,210)(H,167,213)(H,168,185)(H,169,196)(H,170,203)(H,171,207)(H,172,208)(H,173,199)(H,174,214)(H,186,187)(H,188,189)(H4,143,144,145)/t71-,72+,73-,77-,78+,79+,80+,81+,82+,83+,84+,85+,86+,87+,88+,89+,90+,91+,92+,93+,94+,95+,96+,97+,104+,105+,106+,107+,108+,109+,110+/m1/s1
SMILES CC[C@@H](C)[C@H]1C(=N[C@@H](CO)C(=N[C@@H](CO)C(=N[C@@H](C(C)C)C(=N[C@@H](CC(C)C)C(=NCC(=N[C@H]2CSSC[C@H]3C(=NCC(=N[C@@H](CCC(=O)O)C(=N[C@@H](CO)C(=N[C@H]4CSSC[C@@H](C(=N[C@H](CCCCN)C(=N[C@@H](CC(=N)O)C(=N[C@@H](CCCCN)C(=N[C@@H](C(C)C)C(=N[C@@H](CSSC[C@@H](C(=N1)O)N=C([C@@H]1CCCN1C(=O)[C@H]([C@@H](C)CC)N=C([C@H](Cc1ccccc1)N=C([C@H](C(C)C)N=C4O)O)O)O)C(=N[C@@H](Cc1ccc(cc1)O)C(=N[C@@H](CCCNC(=N)N)C(=N[C@@H](CC(=O)O)C(=NCC(=N[C@@H](C(C)C)C(=N[C@@H]([C@H](C)CC)C(=O)N1CCC[C@H]1C(=N3)O)O)O)O)O)O)O)O)O)O)O)O)N=C([C@H](CO)N=C2O)O)O)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   3254.45 Volume:   3114.486
?
Van der Waals volume.
Dense:   1.045 LogP:   -8.072
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -3.986
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.699
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   40.0 Rigid Bonds:   134.0
TPSA:   1319.5
?
Topological Polar Surface Area.
H-Bond Acceptor:   78.0
H-Bond Donor:   46.0 Rings:   9.0
Heavy Atoms:   84.0

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:   9.962 Fsp3:   0.662
MCE-18:   337.229
?
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:   0.343
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.322
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.334
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.815 Promiscuous compounds:   0.149

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.095 MDCK Permeability:   -5.58
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:   0.392
Plasma Protein Binding (PPB):   -7.922% Volume Distribution (VD):   -0.758
Fu: 153.052%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.997 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 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):  -4.649 Half-life (T1/2):  11.472

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:  0.987
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.946 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.007
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  1.0 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.0
BCF:   -0.497
?
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:   3.296
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.786
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.178
?
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
NPO40505 Psychotria leptothyrsa Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[20575512]
NPO40505 Psychotria leptothyrsa Species Rubiaceae 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
NPT5192 Cell line U-937/GTB Homo sapiens IC50 = 3500.0 nM PMID[20575512]

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 NPC485115 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
0.9301 High Similarity NPC486507
0.8919 High Similarity NPC484365
0.8733 High Similarity NPC484964
0.8716 High Similarity NPC477632
0.8716 High Similarity NPC486505
0.84 Intermediate Similarity NPC484963
0.8333 Intermediate Similarity NPC485114
0.8105 Intermediate Similarity NPC485246
0.8052 Intermediate Similarity NPC484078
0.8013 Intermediate Similarity NPC485243
0.7935 Intermediate Similarity NPC485245
0.7636 Intermediate Similarity NPC486506
0.7636 Intermediate Similarity NPC485247
0.7636 Intermediate Similarity NPC486514
0.7622 Intermediate Similarity NPC477635
0.7301 Intermediate Similarity NPC489217
0.7099 Intermediate Similarity NPC482981
0.7086 Intermediate Similarity NPC329843
0.7066 Intermediate Similarity NPC484363
0.6914 Remote Similarity NPC489215
0.6889 Remote Similarity NPC486517
0.6882 Remote Similarity NPC484362
0.6839 Remote Similarity NPC480595
0.6836 Remote Similarity NPC477634
0.6818 Remote Similarity NPC485116
0.678 Remote Similarity NPC477633
0.6761 Remote Similarity NPC489216
0.6559 Remote Similarity NPC479082
0.6497 Remote Similarity NPC480440
0.6452 Remote Similarity NPC479083
0.6424 Remote Similarity NPC481408
0.642 Remote Similarity NPC486515
0.6347 Remote Similarity NPC486513
0.6292 Remote Similarity NPC484965
0.6223 Remote Similarity NPC489512
0.6173 Remote Similarity NPC479131
0.6051 Remote Similarity NPC480596
0.6047 Remote Similarity NPC484364
0.5917 Remote Similarity NPC481409
0.5914 Remote Similarity NPC485244
0.5882 Remote Similarity NPC489549
0.5849 Remote Similarity NPC484875
0.5833 Remote Similarity NPC485242
0.5735 Remote Similarity NPC480594
0.5691 Remote Similarity NPC485125
0.5691 Remote Similarity NPC479141
0.564 Remote Similarity NPC479136
0.5616 Remote Similarity NPC480533
0.56 Remote Similarity NPC61004
0.5574 Remote Similarity NPC486503
0.5526 Remote Similarity NPC329855
0.5497 Remote Similarity NPC479128
0.5491 Remote Similarity NPC485113
0.547 Remote Similarity NPC486508
0.5385 Remote Similarity NPC484880
0.5368 Remote Similarity NPC329847
0.5361 Remote Similarity NPC484882
0.5345 Remote Similarity NPC329295
0.5344 Remote Similarity NPC489511
0.524 Remote Similarity NPC479872
0.5235 Remote Similarity NPC482856
0.5226 Remote Similarity NPC484665
0.5217 Remote Similarity NPC485124
0.5138 Remote Similarity NPC479121
0.511 Remote Similarity NPC320968
0.5094 Remote Similarity NPC484348
0.5074 Remote Similarity NPC486504
0.5062 Remote Similarity NPC479140
0.5028 Remote Similarity NPC479130
0.5028 Remote Similarity NPC479129

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC485115 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