Structure

Physi-Chem Properties

Molecular Weight:  725.54
Volume:  788.698
LogP:  7.783
LogD:  4.907
LogS:  -2.769
# Rotatable Bonds:  33
TPSA:  165.78
# H-Bond Aceptor:  10
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.025
Synthetic Accessibility Score:  4.693
Fsp3:  0.854
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.388
MDCK Permeability:  8.827572855807375e-06
Pgp-inhibitor:  0.224
Pgp-substrate:  0.268
Human Intestinal Absorption (HIA):  0.956
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.028
Plasma Protein Binding (PPB):  96.12860870361328%
Volume Distribution (VD):  1.016
Pgp-substrate:  1.573286533355713%

ADMET: Metabolism

CYP1A2-inhibitor:  0.019
CYP1A2-substrate:  0.102
CYP2C19-inhibitor:  0.29
CYP2C19-substrate:  0.044
CYP2C9-inhibitor:  0.143
CYP2C9-substrate:  0.989
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.022
CYP3A4-inhibitor:  0.186
CYP3A4-substrate:  0.007

ADMET: Excretion

Clearance (CL):  2.332
Half-life (T1/2):  0.251

ADMET: Toxicity

hERG Blockers:  0.323
Human Hepatotoxicity (H-HT):  0.19
Drug-inuced Liver Injury (DILI):  0.017
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.961
Carcinogencity:  0.01
Eye Corrosion:  0.003
Eye Irritation:  0.02
Respiratory Toxicity:  0.128

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC262312

Natural Product ID:  NPC262312
Common Name*:   Chrysogeside B
IUPAC Name:   (E,2R)-2-hydroxy-N-[(2S,3R,4E,8E)-3-hydroxy-9-methyl-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxypentadeca-4,8-dien-2-yl]nonadec-3-enamide
Synonyms:   Chrysogeside B
Standard InCHIKey:  ZVSKJEHFCITPQT-XCEJTAPFSA-N
Standard InCHI:  InChI=1S/C41H75NO9/c1-4-6-8-10-11-12-13-14-15-16-17-18-19-20-24-29-35(45)40(49)42-33(31-50-41-39(48)38(47)37(46)36(30-43)51-41)34(44)28-25-21-23-27-32(3)26-22-9-7-5-2/h24-25,27-29,33-39,41,43-48H,4-23,26,30-31H2,1-3H3,(H,42,49)/b28-25+,29-24+,32-27+/t33-,34+,35+,36+,37+,38-,39+,41+/m0/s1
SMILES:  CCCCCCCCCCCCCCC/C=C/[C@H](C(=N[C@H]([C@@H](/C=C/CC/C=C(/CCCCCC)C)O)CO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1802290
PubChem CID:   53262842
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[1367520]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15974609]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. mycelium n.a. PMID[21381678]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21667925]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22118684]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[26692349]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[33089690]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[8626236]
NPO16076 Penicillium chrysogenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT168 Cell Line P388 Mus musculus IC50 > 50000.0 nM PMID[545554]
NPT165 Cell Line HeLa Homo sapiens IC50 > 50000.0 nM PMID[545554]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 150000.0 nM PMID[545554]
NPT19 Organism Escherichia coli Escherichia coli MIC > 150000.0 nM PMID[545554]
NPT720 Organism Enterobacter aerogenes Enterobacter aerogenes MIC = 1720.0 nM PMID[545554]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC > 150000.0 nM PMID[545554]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 150000.0 nM PMID[545554]
NPT20 Organism Candida albicans Candida albicans MIC > 150000.0 nM PMID[545554]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC262312 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC23454
1.0 High Similarity NPC35269
1.0 High Similarity NPC70323
0.9775 High Similarity NPC45313
0.9773 High Similarity NPC256570
0.9773 High Similarity NPC3568
0.9773 High Similarity NPC17290
0.9773 High Similarity NPC192066
0.977 High Similarity NPC282705
0.977 High Similarity NPC182632
0.9556 High Similarity NPC183449
0.9556 High Similarity NPC197294
0.9556 High Similarity NPC8098
0.9545 High Similarity NPC309898
0.9545 High Similarity NPC475125
0.9545 High Similarity NPC473581
0.9545 High Similarity NPC111567
0.9545 High Similarity NPC263545
0.9545 High Similarity NPC186840
0.9545 High Similarity NPC473950
0.9545 High Similarity NPC473604
0.9545 High Similarity NPC15851
0.9432 High Similarity NPC242503
0.9432 High Similarity NPC74672
0.9432 High Similarity NPC209047
0.9432 High Similarity NPC139782
0.9432 High Similarity NPC43074
0.9333 High Similarity NPC157353
0.9333 High Similarity NPC282088
0.9333 High Similarity NPC156782
0.9333 High Similarity NPC54961
0.9333 High Similarity NPC158445
0.8969 High Similarity NPC201128
0.8901 High Similarity NPC61894
0.8901 High Similarity NPC475603
0.8469 Intermediate Similarity NPC477198
0.7778 Intermediate Similarity NPC475503
0.7692 Intermediate Similarity NPC475918
0.7614 Intermediate Similarity NPC288086
0.7525 Intermediate Similarity NPC475646
0.7447 Intermediate Similarity NPC228638
0.7429 Intermediate Similarity NPC74035
0.7368 Intermediate Similarity NPC476523
0.7339 Intermediate Similarity NPC29501
0.7333 Intermediate Similarity NPC55336
0.7255 Intermediate Similarity NPC189629
0.7212 Intermediate Similarity NPC271207
0.7212 Intermediate Similarity NPC206711
0.7212 Intermediate Similarity NPC255175
0.7212 Intermediate Similarity NPC225978
0.7159 Intermediate Similarity NPC103712
0.7159 Intermediate Similarity NPC291196
0.7155 Intermediate Similarity NPC469943
0.7143 Intermediate Similarity NPC264417
0.7143 Intermediate Similarity NPC217095
0.713 Intermediate Similarity NPC315426
0.7113 Intermediate Similarity NPC73166
0.7111 Intermediate Similarity NPC55652
0.7111 Intermediate Similarity NPC314678
0.7065 Intermediate Similarity NPC229655
0.7033 Intermediate Similarity NPC472174
0.7 Intermediate Similarity NPC39290
0.7 Intermediate Similarity NPC159369
0.6964 Remote Similarity NPC314306
0.6947 Remote Similarity NPC127295
0.6947 Remote Similarity NPC163362
0.6931 Remote Similarity NPC477866
0.6931 Remote Similarity NPC477865
0.6923 Remote Similarity NPC132938
0.6875 Remote Similarity NPC469469
0.6869 Remote Similarity NPC208473
0.6863 Remote Similarity NPC472199
0.6863 Remote Similarity NPC472197
0.6837 Remote Similarity NPC477199
0.6837 Remote Similarity NPC473308
0.6804 Remote Similarity NPC474312
0.6796 Remote Similarity NPC472196
0.6796 Remote Similarity NPC238090
0.6796 Remote Similarity NPC472195
0.6782 Remote Similarity NPC294813
0.6782 Remote Similarity NPC13143
0.6762 Remote Similarity NPC175614
0.6757 Remote Similarity NPC475150
0.6737 Remote Similarity NPC133377
0.6737 Remote Similarity NPC474833
0.6735 Remote Similarity NPC142111
0.6735 Remote Similarity NPC473315
0.6733 Remote Similarity NPC470284
0.6731 Remote Similarity NPC159698
0.6731 Remote Similarity NPC472198
0.6703 Remote Similarity NPC474078
0.6702 Remote Similarity NPC326661
0.6701 Remote Similarity NPC21693
0.6701 Remote Similarity NPC236649
0.6701 Remote Similarity NPC280367
0.6667 Remote Similarity NPC472173
0.6667 Remote Similarity NPC469865
0.6636 Remote Similarity NPC313440
0.6634 Remote Similarity NPC475186
0.6634 Remote Similarity NPC125142
0.6634 Remote Similarity NPC118077
0.6633 Remote Similarity NPC251026
0.6632 Remote Similarity NPC110813
0.6612 Remote Similarity NPC313342
0.6612 Remote Similarity NPC314512
0.6612 Remote Similarity NPC313333
0.6612 Remote Similarity NPC314451
0.6598 Remote Similarity NPC100697
0.6585 Remote Similarity NPC329919
0.6585 Remote Similarity NPC477793
0.6581 Remote Similarity NPC6531
0.6569 Remote Similarity NPC470137
0.6566 Remote Similarity NPC156089
0.6566 Remote Similarity NPC473500
0.6566 Remote Similarity NPC38295
0.6566 Remote Similarity NPC470313
0.6562 Remote Similarity NPC316807
0.6538 Remote Similarity NPC208537
0.6538 Remote Similarity NPC270005
0.6531 Remote Similarity NPC82799
0.6522 Remote Similarity NPC273215
0.6522 Remote Similarity NPC295444
0.6522 Remote Similarity NPC279383
0.6522 Remote Similarity NPC268327
0.6517 Remote Similarity NPC147292
0.65 Remote Similarity NPC220167
0.65 Remote Similarity NPC266718
0.65 Remote Similarity NPC136699
0.65 Remote Similarity NPC475035
0.6496 Remote Similarity NPC30196
0.6476 Remote Similarity NPC320089
0.6476 Remote Similarity NPC320552
0.6475 Remote Similarity NPC204639
0.6471 Remote Similarity NPC477515
0.6471 Remote Similarity NPC475037
0.6471 Remote Similarity NPC314268
0.6471 Remote Similarity NPC67917
0.6471 Remote Similarity NPC313802
0.6465 Remote Similarity NPC477390
0.6465 Remote Similarity NPC20072
0.6465 Remote Similarity NPC477385
0.6446 Remote Similarity NPC273185
0.6444 Remote Similarity NPC315141
0.6444 Remote Similarity NPC129995
0.6442 Remote Similarity NPC118078
0.6442 Remote Similarity NPC327253
0.6442 Remote Similarity NPC473311
0.6437 Remote Similarity NPC155457
0.6436 Remote Similarity NPC470124
0.6429 Remote Similarity NPC133226
0.6429 Remote Similarity NPC470147
0.6422 Remote Similarity NPC64348
0.6415 Remote Similarity NPC470283
0.6413 Remote Similarity NPC280065
0.6413 Remote Similarity NPC45060
0.6408 Remote Similarity NPC248312
0.6408 Remote Similarity NPC137368
0.6404 Remote Similarity NPC473578
0.6404 Remote Similarity NPC133625
0.64 Remote Similarity NPC313962
0.6389 Remote Similarity NPC240372
0.6381 Remote Similarity NPC302584
0.6379 Remote Similarity NPC1111
0.6379 Remote Similarity NPC261750
0.6378 Remote Similarity NPC314361
0.6371 Remote Similarity NPC314282
0.6364 Remote Similarity NPC29468
0.6355 Remote Similarity NPC189764
0.6346 Remote Similarity NPC249408
0.6346 Remote Similarity NPC104129
0.6346 Remote Similarity NPC285588
0.6333 Remote Similarity NPC477525
0.6328 Remote Similarity NPC78189
0.6327 Remote Similarity NPC470148
0.6327 Remote Similarity NPC470149
0.6327 Remote Similarity NPC180725
0.6325 Remote Similarity NPC475988
0.6321 Remote Similarity NPC280390
0.6304 Remote Similarity NPC249713
0.6299 Remote Similarity NPC475472
0.6299 Remote Similarity NPC139585
0.6296 Remote Similarity NPC90583
0.629 Remote Similarity NPC315058
0.6286 Remote Similarity NPC202886
0.6275 Remote Similarity NPC471494
0.6275 Remote Similarity NPC470658
0.6275 Remote Similarity NPC475034
0.6273 Remote Similarity NPC469942
0.6261 Remote Similarity NPC474891
0.626 Remote Similarity NPC315783
0.626 Remote Similarity NPC314629
0.625 Remote Similarity NPC73829
0.625 Remote Similarity NPC316186
0.625 Remote Similarity NPC130807
0.625 Remote Similarity NPC119794
0.6239 Remote Similarity NPC60432
0.6239 Remote Similarity NPC474194
0.6237 Remote Similarity NPC223174
0.6237 Remote Similarity NPC327486
0.6237 Remote Similarity NPC327753

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC262312 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9432 High Similarity NPD8522 Clinical (unspecified phase)
0.7091 Intermediate Similarity NPD6421 Discontinued
0.7009 Intermediate Similarity NPD1407 Approved
0.6964 Remote Similarity NPD6430 Approved
0.6964 Remote Similarity NPD6429 Approved
0.6612 Remote Similarity NPD8341 Approved
0.6612 Remote Similarity NPD8340 Approved
0.6612 Remote Similarity NPD8342 Approved
0.6612 Remote Similarity NPD8299 Approved
0.6577 Remote Similarity NPD5357 Phase 1
0.6446 Remote Similarity NPD6436 Phase 3
0.6423 Remote Similarity NPD8451 Approved
0.6387 Remote Similarity NPD7641 Discontinued
0.6371 Remote Similarity NPD8448 Approved
0.6364 Remote Similarity NPD8444 Approved
0.626 Remote Similarity NPD7829 Approved
0.626 Remote Similarity NPD7830 Approved
0.6237 Remote Similarity NPD9445 Approved
0.622 Remote Similarity NPD8392 Approved
0.622 Remote Similarity NPD8390 Approved
0.622 Remote Similarity NPD8391 Approved
0.614 Remote Similarity NPD6640 Phase 3
0.6129 Remote Similarity NPD7642 Approved
0.6111 Remote Similarity NPD8074 Phase 3
0.6038 Remote Similarity NPD3716 Discontinued
0.6036 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6033 Remote Similarity NPD7505 Discontinued
0.6033 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6 Remote Similarity NPD6428 Approved
0.6 Remote Similarity NPD7839 Suspended
0.6 Remote Similarity NPD4211 Phase 1
0.6 Remote Similarity NPD4759 Clinical (unspecified phase)
0.5934 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5926 Remote Similarity NPD7983 Approved
0.5917 Remote Similarity NPD3731 Phase 3
0.5909 Remote Similarity NPD5381 Approved
0.5909 Remote Similarity NPD5378 Approved
0.5909 Remote Similarity NPD5377 Approved
0.584 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5833 Remote Similarity NPD3168 Discontinued
0.5833 Remote Similarity NPD7838 Discovery
0.5833 Remote Similarity NPD6698 Approved
0.5833 Remote Similarity NPD46 Approved
0.5826 Remote Similarity NPD8045 Clinical (unspecified phase)
0.582 Remote Similarity NPD4832 Approved
0.582 Remote Similarity NPD4831 Approved
0.582 Remote Similarity NPD4830 Approved
0.5794 Remote Similarity NPD8080 Discontinued
0.5781 Remote Similarity NPD8273 Phase 1
0.5772 Remote Similarity NPD7500 Approved
0.5763 Remote Similarity NPD8174 Phase 2
0.575 Remote Similarity NPD8413 Clinical (unspecified phase)
0.575 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5726 Remote Similarity NPD5376 Approved
0.5725 Remote Similarity NPD6914 Discontinued
0.567 Remote Similarity NPD3212 Clinical (unspecified phase)
0.563 Remote Similarity NPD8387 Clinical (unspecified phase)
0.563 Remote Similarity NPD6686 Approved
0.5625 Remote Similarity NPD7844 Discontinued

  Bioactivity similarity: Similar Natural Products in NPASS

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