Natural Product: NPC488733

Natural Product IDNPC488733
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
HNHSBQSERBHUQW-BUQDZIJCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 132566453
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 HNHSBQSERBHUQW-BUQDZIJCSA-N
Standard InCHI InChI=1S/C72H72O36/c1-23-49(83)57(91)65(71(99-23)105-63-53(87)45-37(81)17-31(75)19-39(45)101-61(63)27-7-13-33(77)35(79)15-27)107-69-59(93)55(89)51(85)41(103-69)21-97-67(95)47-43(25-3-9-29(73)10-4-25)44(26-5-11-30(74)12-6-26)48(47)68(96)98-22-42-52(86)56(90)60(94)70(104-42)108-66-58(92)50(84)24(2)100-72(66)106-64-54(88)46-38(82)18-32(76)20-40(46)102-62(64)28-8-14-34(78)36(80)16-28/h3-20,23-24,41-44,47-52,55-60,65-66,69-86,89-94H,21-22H2,1-2H3/t23-,24-,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(c(c1)O)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(c(c2)O)O)O)O)O)O)O)O)O)O1)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1512.38 Volume:   1395.807
?
Van der Waals volume.
Dense:   1.084 LogP:   0.738
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.354
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.124
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   20.0 Rigid Bonds:   78.0
TPSA:   591.46
?
Topological Polar Surface Area.
H-Bond Acceptor:   36.0
H-Bond Donor:   20.0 Rings:   13.0
Heavy Atoms:   36.0

MedChem Properties

QED Drug-Likeness Score:   0.04 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.433 Fsp3:   0.389
MCE-18:   309.72
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.859 Fluc inhibitor:   0.261
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.616
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.662
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.365 Promiscuous compounds:   0.554

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.777 MDCK Permeability:   -4.896
Pgp-inhibitor:   0.0 Pgp-substrate:   0.358
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):   0.002
20% Bioavailability (F20%):   0.999 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.001
Plasma Protein Binding (PPB):   83.489% Volume Distribution (VD):   0.034
Fu: 10.745%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.044
BSEP inhibitor:   0.003

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:   0.965
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.038
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.622
?
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):  -0.436 Half-life (T1/2):  9.78

ADMET: Toxicity

hERG Blockers:  0.004 hERG Blockers (10um):  0.363
Human Hepatotoxicity (H-HT):  0.233 Drug-induced Liver Injury (DILI):  0.996
AMES Toxicity:  0.914 Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.308 Skin Sensitization:  1.0
Carcinogencity:  0.002 Eye Corrosion:  0.0
Eye Irritation:  0.011 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.001 Drug-induced Nephrotoxicity:  0.113
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.091
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.994
BCF:   0.707
?
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:   4.149
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.237
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.96
?
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 NPC488733 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 NPC488736
0.9794 High Similarity NPC488737
0.9381 High Similarity NPC488734
0.9381 High Similarity NPC488735
0.9381 High Similarity NPC488732
0.9381 High Similarity NPC488738
0.8812 High Similarity NPC488740
0.8252 Intermediate Similarity NPC488739
0.7216 Intermediate Similarity NPC95866
0.7157 Intermediate Similarity NPC122467
0.6768 Remote Similarity NPC476215
0.6731 Remote Similarity NPC12013
0.6731 Remote Similarity NPC11432
0.6731 Remote Similarity NPC477613
0.6698 Remote Similarity NPC89127
0.6609 Remote Similarity NPC480444
0.6602 Remote Similarity NPC155877
0.6542 Remote Similarity NPC471669
0.6522 Remote Similarity NPC162394
0.6471 Remote Similarity NPC21359
0.6471 Remote Similarity NPC460984
0.6429 Remote Similarity NPC303694
0.6422 Remote Similarity NPC602448
0.6373 Remote Similarity NPC254855
0.6373 Remote Similarity NPC116864
0.6373 Remote Similarity NPC244776
0.6373 Remote Similarity NPC94610
0.6341 Remote Similarity NPC487502
0.633 Remote Similarity NPC221342
0.633 Remote Similarity NPC476470
0.6293 Remote Similarity NPC480445
0.6286 Remote Similarity NPC203259
0.6286 Remote Similarity NPC33054
0.6286 Remote Similarity NPC176740
0.6286 Remote Similarity NPC471725
0.6286 Remote Similarity NPC134532
0.6286 Remote Similarity NPC602582
0.623 Remote Similarity NPC473554
0.619 Remote Similarity NPC163242
0.619 Remote Similarity NPC272068
0.6161 Remote Similarity NPC89052
0.6148 Remote Similarity NPC487499
0.6126 Remote Similarity NPC223426
0.6116 Remote Similarity NPC25946
0.6075 Remote Similarity NPC255157
0.6075 Remote Similarity NPC35167
0.6075 Remote Similarity NPC259896
0.604 Remote Similarity NPC216496
0.5962 Remote Similarity NPC170052
0.5962 Remote Similarity NPC135846
0.5906 Remote Similarity NPC249560
0.5893 Remote Similarity NPC292929
0.5888 Remote Similarity NPC173582
0.5888 Remote Similarity NPC265885
0.5888 Remote Similarity NPC181465
0.5888 Remote Similarity NPC67326
0.5888 Remote Similarity NPC215710
0.5888 Remote Similarity NPC473438
0.5888 Remote Similarity NPC253788
0.5873 Remote Similarity NPC30011
0.5846 Remote Similarity NPC487501
0.5833 Remote Similarity NPC156869
0.5789 Remote Similarity NPC81042
0.5776 Remote Similarity NPC173837
0.5769 Remote Similarity NPC487500
0.5743 Remote Similarity NPC127546
0.5743 Remote Similarity NPC57625
0.5743 Remote Similarity NPC173637
0.5743 Remote Similarity NPC317489
0.5743 Remote Similarity NPC223424
0.5743 Remote Similarity NPC600591
0.5741 Remote Similarity NPC470405
0.5702 Remote Similarity NPC218161
0.5688 Remote Similarity NPC304741
0.5664 Remote Similarity NPC85751
0.5664 Remote Similarity NPC19240
0.5664 Remote Similarity NPC220173
0.5645 Remote Similarity NPC480442
0.5641 Remote Similarity NPC292019
0.5641 Remote Similarity NPC202908
0.5625 Remote Similarity NPC72554
0.5625 Remote Similarity NPC473327
0.561 Remote Similarity NPC241781
0.5596 Remote Similarity NPC39834
0.5591 Remote Similarity NPC275977
0.5575 Remote Similarity NPC97119
0.5575 Remote Similarity NPC142142
0.5574 Remote Similarity NPC156785
0.5545 Remote Similarity NPC605592
0.5517 Remote Similarity NPC214621
0.5517 Remote Similarity NPC34267
0.5505 Remote Similarity NPC258044
0.5505 Remote Similarity NPC217387
0.5505 Remote Similarity NPC471079
0.5495 Remote Similarity NPC129264
0.5487 Remote Similarity NPC37668
0.5469 Remote Similarity NPC231787
0.5462 Remote Similarity NPC480441
0.5455 Remote Similarity NPC97817
0.5455 Remote Similarity NPC471748
0.5446 Remote Similarity NPC153755
0.544 Remote Similarity NPC192539
0.5391 Remote Similarity NPC476472
0.5391 Remote Similarity NPC294815
0.5391 Remote Similarity NPC16194
0.5378 Remote Similarity NPC477895
0.5377 Remote Similarity NPC175107
0.536 Remote Similarity NPC209550
0.5345 Remote Similarity NPC470445
0.534 Remote Similarity NPC111929
0.534 Remote Similarity NPC320283
0.534 Remote Similarity NPC41121
0.5333 Remote Similarity NPC217520
0.5327 Remote Similarity NPC224530
0.5317 Remote Similarity NPC480443
0.531 Remote Similarity NPC253521
0.531 Remote Similarity NPC470125
0.531 Remote Similarity NPC113836
0.5304 Remote Similarity NPC603079
0.5299 Remote Similarity NPC470450
0.5294 Remote Similarity NPC189564
0.5259 Remote Similarity NPC76831
0.5238 Remote Similarity NPC145038
0.5238 Remote Similarity NPC56077
0.5238 Remote Similarity NPC281131
0.5238 Remote Similarity NPC253662
0.5238 Remote Similarity NPC179950
0.5238 Remote Similarity NPC88789
0.5238 Remote Similarity NPC491374
0.5225 Remote Similarity NPC29958
0.5225 Remote Similarity NPC609888
0.5221 Remote Similarity NPC144097
0.5217 Remote Similarity NPC270448
0.521 Remote Similarity NPC203145
0.5207 Remote Similarity NPC25523
0.5185 Remote Similarity NPC259957
0.5175 Remote Similarity NPC126784
0.5175 Remote Similarity NPC240306
0.5175 Remote Similarity NPC241423
0.5175 Remote Similarity NPC154741
0.5146 Remote Similarity NPC276222
0.5146 Remote Similarity NPC274618
0.5146 Remote Similarity NPC118284
0.5146 Remote Similarity NPC608147
0.5124 Remote Similarity NPC219043
0.5122 Remote Similarity NPC139571
0.5108 Remote Similarity NPC33083
0.5096 Remote Similarity NPC67037
0.5096 Remote Similarity NPC255615
0.5093 Remote Similarity NPC219904
0.5093 Remote Similarity NPC48093
0.5089 Remote Similarity NPC139320
0.5088 Remote Similarity NPC470444
0.5085 Remote Similarity NPC287889
0.5048 Remote Similarity NPC135599
0.5048 Remote Similarity NPC73855
0.5048 Remote Similarity NPC113968
0.5048 Remote Similarity NPC328940
0.5048 Remote Similarity NPC277174
0.5048 Remote Similarity NPC606877
0.5043 Remote Similarity NPC221288
0.5043 Remote Similarity NPC61904
0.5043 Remote Similarity NPC194836
0.5043 Remote Similarity NPC91493
0.5043 Remote Similarity NPC605081

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488733 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
0.6286 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