Natural Product: NPC488735

Natural Product IDNPC488735
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
GAZFVUIZWWQAEQ-VKVZZMADSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 132566455
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 GAZFVUIZWWQAEQ-VKVZZMADSA-N
Standard InCHI InChI=1S/C72H72O34/c1-25-49(81)57(89)65(71(97-25)103-63-53(85)45-37(79)19-35(77)21-39(45)99-61(63)29-7-15-33(75)16-8-29)105-69-59(91)55(87)51(83)41(101-69)23-95-67(93)47-43(27-3-11-31(73)12-4-27)44(28-5-13-32(74)14-6-28)48(47)68(94)96-24-42-52(84)56(88)60(92)70(102-42)106-66-58(90)50(82)26(2)98-72(66)104-64-54(86)46-38(80)20-36(78)22-40(46)100-62(64)30-9-17-34(76)18-10-30/h3-22,25-26,41-44,47-52,55-60,65-66,69-84,87-92H,23-24H2,1-2H3/t25-,26-,41+,42+,43-,44-,47+,48+,49-,50-,51+,52+,55-,56-,57+,58+,59+,60+,65+,66+,69-,70-,71-,72-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(cc1)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)[C@@H]2[C@@H](c3ccc(cc3)O)[C@H](c3ccc(cc3)O)[C@H]2C(=O)OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)O[C@@H]2[C@@H]([C@H]([C@H](C)O[C@H]2Oc2c(=O)c3c(cc(cc3oc2c2ccc(cc2)O)O)O)O)O)O)O)O)O1)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1480.39 Volume:   1378.226
?
Van der Waals volume.
Dense:   1.074 LogP:   1.143
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.006
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.846
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   20.0 Rigid Bonds:   78.0
TPSA:   551.0
?
Topological Polar Surface Area.
H-Bond Acceptor:   34.0
H-Bond Donor:   18.0 Rings:   13.0
Heavy Atoms:   34.0

MedChem Properties

QED Drug-Likeness Score:   0.052 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.276 Fsp3:   0.389
MCE-18:   302.76
?
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:   0.859 Fluc inhibitor:   0.38
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.563
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.66
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.363 Promiscuous compounds:   0.544

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.906 MDCK Permeability:   -4.777
Pgp-inhibitor:   0.0 Pgp-substrate:   0.969
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):   0.0
20% Bioavailability (F20%):   0.636 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.002
Plasma Protein Binding (PPB):   84.783% Volume Distribution (VD):   0.042
Fu: 9.587%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.356
BSEP inhibitor:   0.33

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.964
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.42
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.693
?
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):  -0.705 Half-life (T1/2):  9.364

ADMET: Toxicity

hERG Blockers:  0.011 hERG Blockers (10um):  0.291
Human Hepatotoxicity (H-HT):  0.318 Drug-induced Liver Injury (DILI):  0.993
AMES Toxicity:  0.854 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.422 Skin Sensitization:  1.0
Carcinogencity:  0.004 Eye Corrosion:  0.0
Eye Irritation:  0.003 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.995
Hematotoxicity:  0.001 Drug-induced Nephrotoxicity:  0.228
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.228
A549 Cytotoxicity:  0.993 Hek293 Cytotoxicity:  1.0
BCF:   0.783
?
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:   4.161
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.003
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.731
?
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
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaves n.a. n.a. PMID[27140807]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves n.a. n.a. PMID[33127538]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota fresh sarcotestas Kwanak Campus of Seoul National University, Seoul, Korea 1996-Sep PMID[9677265]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves St. Louis 1996-SEP PMID[9834151]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. PMID[9834158]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Wood n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. Database[FooDB]

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
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 100000.0 nM PMID[27140807]

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 NPC488735 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
1.0 High Similarity NPC488734
1.0 High Similarity NPC488732
1.0 High Similarity NPC488738
0.9588 High Similarity NPC488737
0.9381 High Similarity NPC488736
0.9381 High Similarity NPC488733
0.8788 High Similarity NPC488739
0.8252 Intermediate Similarity NPC488740
0.7263 Intermediate Similarity NPC476215
0.72 Intermediate Similarity NPC12013
0.72 Intermediate Similarity NPC11432
0.72 Intermediate Similarity NPC477613
0.6857 Remote Similarity NPC602448
0.6762 Remote Similarity NPC221342
0.6762 Remote Similarity NPC476470
0.6696 Remote Similarity NPC480445
0.6667 Remote Similarity NPC95866
0.6635 Remote Similarity NPC122467
0.6634 Remote Similarity NPC163242
0.6634 Remote Similarity NPC272068
0.661 Remote Similarity NPC473554
0.6496 Remote Similarity NPC25946
0.6495 Remote Similarity NPC216496
0.64 Remote Similarity NPC170052
0.64 Remote Similarity NPC135846
0.6311 Remote Similarity NPC173582
0.6311 Remote Similarity NPC265885
0.6311 Remote Similarity NPC181465
0.6311 Remote Similarity NPC215710
0.6311 Remote Similarity NPC473438
0.6311 Remote Similarity NPC253788
0.6296 Remote Similarity NPC292929
0.6293 Remote Similarity NPC480444
0.6273 Remote Similarity NPC89052
0.6204 Remote Similarity NPC89127
0.6154 Remote Similarity NPC470405
0.6095 Remote Similarity NPC155877
0.6095 Remote Similarity NPC304741
0.6091 Remote Similarity NPC218161
0.6068 Remote Similarity NPC162394
0.6055 Remote Similarity NPC85751
0.6055 Remote Similarity NPC471669
0.6055 Remote Similarity NPC19240
0.6033 Remote Similarity NPC21359
0.6033 Remote Similarity NPC460984
0.5965 Remote Similarity NPC303694
0.5963 Remote Similarity NPC142142
0.592 Remote Similarity NPC487502
0.5905 Remote Similarity NPC471079
0.5888 Remote Similarity NPC129264
0.5877 Remote Similarity NPC173837
0.5865 Remote Similarity NPC254855
0.5865 Remote Similarity NPC116864
0.5865 Remote Similarity NPC244776
0.5865 Remote Similarity NPC94610
0.5806 Remote Similarity NPC231787
0.5794 Remote Similarity NPC203259
0.5794 Remote Similarity NPC33054
0.5794 Remote Similarity NPC176740
0.5794 Remote Similarity NPC471725
0.5794 Remote Similarity NPC134532
0.5794 Remote Similarity NPC602582
0.5766 Remote Similarity NPC220173
0.5758 Remote Similarity NPC111929
0.5758 Remote Similarity NPC320283
0.5758 Remote Similarity NPC41121
0.5752 Remote Similarity NPC214621
0.5752 Remote Similarity NPC34267
0.5728 Remote Similarity NPC224530
0.5726 Remote Similarity NPC487499
0.5702 Remote Similarity NPC209550
0.5688 Remote Similarity NPC470125
0.5664 Remote Similarity NPC223426
0.5664 Remote Similarity NPC470450
0.5656 Remote Similarity NPC480443
0.5652 Remote Similarity NPC189564
0.5596 Remote Similarity NPC255157
0.5596 Remote Similarity NPC35167
0.5596 Remote Similarity NPC259896
0.5586 Remote Similarity NPC473327
0.5565 Remote Similarity NPC203145
0.5556 Remote Similarity NPC25523
0.5545 Remote Similarity NPC240306
0.5545 Remote Similarity NPC153755
0.5536 Remote Similarity NPC603079
0.5528 Remote Similarity NPC192539
0.5504 Remote Similarity NPC249560
0.5487 Remote Similarity NPC476472
0.5487 Remote Similarity NPC294815
0.5487 Remote Similarity NPC16194
0.5487 Remote Similarity NPC76831
0.5481 Remote Similarity NPC48093
0.547 Remote Similarity NPC477895
0.5469 Remote Similarity NPC30011
0.5463 Remote Similarity NPC139320
0.5455 Remote Similarity NPC487501
0.5455 Remote Similarity NPC470444
0.5446 Remote Similarity NPC270448
0.5429 Remote Similarity NPC259957
0.5424 Remote Similarity NPC217520
0.5413 Remote Similarity NPC67326
0.5413 Remote Similarity NPC39834
0.5379 Remote Similarity NPC487500
0.5364 Remote Similarity NPC156869
0.5351 Remote Similarity NPC470447
0.5345 Remote Similarity NPC81042
0.5321 Remote Similarity NPC258044
0.5321 Remote Similarity NPC217387
0.5321 Remote Similarity NPC609888
0.531 Remote Similarity NPC32641
0.531 Remote Similarity NPC256188
0.531 Remote Similarity NPC35119
0.5285 Remote Similarity NPC474522
0.5268 Remote Similarity NPC61904
0.5263 Remote Similarity NPC101399
0.5263 Remote Similarity NPC221288
0.5263 Remote Similarity NPC217822
0.5263 Remote Similarity NPC11847
0.5263 Remote Similarity NPC198938
0.5263 Remote Similarity NPC194836
0.5263 Remote Similarity NPC91493
0.5263 Remote Similarity NPC605081
0.5243 Remote Similarity NPC127546
0.5243 Remote Similarity NPC57625
0.5243 Remote Similarity NPC77672
0.5243 Remote Similarity NPC133671
0.5243 Remote Similarity NPC135391
0.5243 Remote Similarity NPC173637
0.5243 Remote Similarity NPC78263
0.5243 Remote Similarity NPC317489
0.5243 Remote Similarity NPC250069
0.5243 Remote Similarity NPC223424
0.5243 Remote Similarity NPC600591
0.5238 Remote Similarity NPC480442
0.5231 Remote Similarity NPC72554
0.5225 Remote Similarity NPC65563
0.5225 Remote Similarity NPC470949
0.521 Remote Similarity NPC219043
0.521 Remote Similarity NPC292019
0.521 Remote Similarity NPC202908
0.52 Remote Similarity NPC241781
0.5194 Remote Similarity NPC275977
0.5189 Remote Similarity NPC159579
0.5179 Remote Similarity NPC473571
0.5179 Remote Similarity NPC110941
0.5179 Remote Similarity NPC186816
0.5172 Remote Similarity NPC287889
0.5167 Remote Similarity NPC470712
0.5161 Remote Similarity NPC156785
0.5149 Remote Similarity NPC54802
0.5149 Remote Similarity NPC197304
0.5133 Remote Similarity NPC296018
0.513 Remote Similarity NPC97119
0.5098 Remote Similarity NPC288084
0.5096 Remote Similarity NPC104677
0.5089 Remote Similarity NPC605592
0.5085 Remote Similarity NPC96605
0.5085 Remote Similarity NPC280642
0.5083 Remote Similarity NPC48984
0.5082 Remote Similarity NPC139571
0.5075 Remote Similarity NPC97817
0.5047 Remote Similarity NPC219904
0.5047 Remote Similarity NPC129217
0.5043 Remote Similarity NPC37668
0.5043 Remote Similarity NPC36138
0.5043 Remote Similarity NPC104883
0.5043 Remote Similarity NPC488679
0.5041 Remote Similarity NPC480441

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488735 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
0.5794 Remote Similarity NPD6797 Phase 2

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