Structure

Physi-Chem Properties

Molecular Weight:  751.56
Volume:  820.654
LogP:  7.241
LogD:  4.648
LogS:  -2.903
# Rotatable Bonds:  34
TPSA:  165.78
# H-Bond Aceptor:  10
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.017
Synthetic Accessibility Score:  4.837
Fsp3:  0.814
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:  -5.413
MDCK Permeability:  2.1565583665505983e-05
Pgp-inhibitor:  0.018
Pgp-substrate:  0.113
Human Intestinal Absorption (HIA):  0.773
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.014
Plasma Protein Binding (PPB):  97.87024688720703%
Volume Distribution (VD):  1.187
Pgp-substrate:  1.8231686353683472%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.121
CYP2C19-inhibitor:  0.266
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.187
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.12
CYP3A4-inhibitor:  0.354
CYP3A4-substrate:  0.012

ADMET: Excretion

Clearance (CL):  1.777
Half-life (T1/2):  0.269

ADMET: Toxicity

hERG Blockers:  0.416
Human Hepatotoxicity (H-HT):  0.202
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.153
Rat Oral Acute Toxicity:  0.029
Maximum Recommended Daily Dose:  0.051
Skin Sensitization:  0.965
Carcinogencity:  0.018
Eye Corrosion:  0.003
Eye Irritation:  0.021
Respiratory Toxicity:  0.102

Download Data

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

  Natural Product: NPC45313

Natural Product ID:  NPC45313
Common Name*:   Sarcoehrenoside A
IUPAC Name:   (E,2R)-2-hydroxy-N-[(2S,3R,4E,8E,10E)-3-hydroxy-9-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoctadeca-4,8,10-trien-2-yl]octadec-3-enamide
Synonyms:  
Standard InCHIKey:  FWPRXLLJDAFCIU-QADPEEHDSA-N
Standard InCHI:  InChI=1S/C43H77NO9/c1-4-6-8-10-12-13-14-15-16-17-18-20-22-26-31-37(47)42(51)44-35(33-52-43-41(50)40(49)39(48)38(32-45)53-43)36(46)30-27-23-25-29-34(3)28-24-21-19-11-9-7-5-2/h24,26-31,35-41,43,45-50H,4-23,25,32-33H2,1-3H3,(H,44,51)/b28-24+,30-27+,31-26+,34-29+/t35-,36+,37+,38+,39+,40-,41+,43-/m0/s1
SMILES:  CCCCCCCCCCCCCC/C=C/[C@H](C(=N[C@@H](CO[C@@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)[C@@H](/C=C/CC/C=C(C)/C=C/CCCCCCC)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL552726
PubChem CID:   45271338
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000257] Sphingolipids
        • [CHEMONTID:0003258] Glycosphingolipids
          • [CHEMONTID:0001419] Neutral glycosphingolipids
            • [CHEMONTID:0001428] Simple glycosylceramides
              • [CHEMONTID:0004305] Glycosyl-N-acylsphingosines

*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
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[19006372]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[20099902]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[25075977]
NPO15453 Sarcophyton ehrenbergi Species Alcyoniidae 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
NPT113 Cell Line RAW264.7 Mus musculus Activity = 47.3 % PMID[564039]

☑ 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 NPC45313 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
0.9778 High Similarity NPC8098
0.9778 High Similarity NPC183449
0.9778 High Similarity NPC197294
0.9775 High Similarity NPC262312
0.9775 High Similarity NPC70323
0.9775 High Similarity NPC35269
0.9775 High Similarity NPC23454
0.9556 High Similarity NPC192066
0.9556 High Similarity NPC17290
0.9556 High Similarity NPC54961
0.9556 High Similarity NPC282088
0.9556 High Similarity NPC156782
0.9556 High Similarity NPC3568
0.9556 High Similarity NPC157353
0.9556 High Similarity NPC256570
0.9556 High Similarity NPC158445
0.9551 High Similarity NPC182632
0.9551 High Similarity NPC282705
0.9333 High Similarity NPC473950
0.9333 High Similarity NPC186840
0.9333 High Similarity NPC473604
0.9333 High Similarity NPC15851
0.9333 High Similarity NPC475125
0.9333 High Similarity NPC111567
0.9333 High Similarity NPC263545
0.9333 High Similarity NPC473581
0.9333 High Similarity NPC309898
0.9222 High Similarity NPC74672
0.9222 High Similarity NPC139782
0.9222 High Similarity NPC209047
0.9222 High Similarity NPC43074
0.9222 High Similarity NPC242503
0.8788 High Similarity NPC201128
0.871 High Similarity NPC61894
0.871 High Similarity NPC475603
0.83 Intermediate Similarity NPC477198
0.7624 Intermediate Similarity NPC475503
0.7547 Intermediate Similarity NPC475918
0.7524 Intermediate Similarity NPC55336
0.7523 Intermediate Similarity NPC29501
0.7444 Intermediate Similarity NPC288086
0.7379 Intermediate Similarity NPC475646
0.7333 Intermediate Similarity NPC314678
0.7315 Intermediate Similarity NPC315426
0.7292 Intermediate Similarity NPC228638
0.729 Intermediate Similarity NPC74035
0.7216 Intermediate Similarity NPC476523
0.7129 Intermediate Similarity NPC477866
0.7129 Intermediate Similarity NPC477865
0.7115 Intermediate Similarity NPC189629
0.7075 Intermediate Similarity NPC271207
0.7075 Intermediate Similarity NPC225978
0.7075 Intermediate Similarity NPC255175
0.7075 Intermediate Similarity NPC206711
0.7071 Intermediate Similarity NPC208473
0.7041 Intermediate Similarity NPC473308
0.7034 Intermediate Similarity NPC469943
0.7 Intermediate Similarity NPC103712
0.7 Intermediate Similarity NPC291196
0.6989 Remote Similarity NPC264417
0.6989 Remote Similarity NPC217095
0.697 Remote Similarity NPC73166
0.6957 Remote Similarity NPC55652
0.6952 Remote Similarity NPC175614
0.6939 Remote Similarity NPC142111
0.6939 Remote Similarity NPC473315
0.6915 Remote Similarity NPC229655
0.6882 Remote Similarity NPC472174
0.6882 Remote Similarity NPC472173
0.6863 Remote Similarity NPC39290
0.6863 Remote Similarity NPC159369
0.6842 Remote Similarity NPC314306
0.6837 Remote Similarity NPC251026
0.6832 Remote Similarity NPC475186
0.6832 Remote Similarity NPC118077
0.6804 Remote Similarity NPC127295
0.6804 Remote Similarity NPC163362
0.6777 Remote Similarity NPC313333
0.6777 Remote Similarity NPC314451
0.6777 Remote Similarity NPC314512
0.6777 Remote Similarity NPC313342
0.6774 Remote Similarity NPC132938
0.6765 Remote Similarity NPC470137
0.6748 Remote Similarity NPC329919
0.6748 Remote Similarity NPC477793
0.6735 Remote Similarity NPC469469
0.6731 Remote Similarity NPC472199
0.6731 Remote Similarity NPC472197
0.67 Remote Similarity NPC477199
0.6667 Remote Similarity NPC477385
0.6667 Remote Similarity NPC472196
0.6667 Remote Similarity NPC315141
0.6667 Remote Similarity NPC477390
0.6667 Remote Similarity NPC129995
0.6667 Remote Similarity NPC320552
0.6667 Remote Similarity NPC472195
0.6667 Remote Similarity NPC238090
0.6667 Remote Similarity NPC474312
0.6639 Remote Similarity NPC67917
0.6639 Remote Similarity NPC314268
0.6639 Remote Similarity NPC313802
0.6639 Remote Similarity NPC477515
0.6637 Remote Similarity NPC475150
0.6635 Remote Similarity NPC327253
0.6635 Remote Similarity NPC473311
0.6629 Remote Similarity NPC294813
0.6629 Remote Similarity NPC13143
0.6604 Remote Similarity NPC159698
0.6604 Remote Similarity NPC472198
0.6602 Remote Similarity NPC470284
0.6598 Remote Similarity NPC133377
0.6598 Remote Similarity NPC474833
0.6579 Remote Similarity NPC133625
0.6566 Remote Similarity NPC236649
0.6566 Remote Similarity NPC21693
0.6566 Remote Similarity NPC280367
0.6562 Remote Similarity NPC326661
0.6559 Remote Similarity NPC474078
0.6556 Remote Similarity NPC477525
0.6552 Remote Similarity NPC469865
0.6542 Remote Similarity NPC189764
0.6538 Remote Similarity NPC285588
0.6535 Remote Similarity NPC314361
0.6532 Remote Similarity NPC314282
0.6514 Remote Similarity NPC313440
0.6505 Remote Similarity NPC125142
0.6495 Remote Similarity NPC110813
0.6484 Remote Similarity NPC78189
0.6471 Remote Similarity NPC6531
0.6465 Remote Similarity NPC100697
0.6442 Remote Similarity NPC316186
0.6436 Remote Similarity NPC38295
0.6436 Remote Similarity NPC470313
0.6436 Remote Similarity NPC156089
0.6436 Remote Similarity NPC473500
0.6429 Remote Similarity NPC316807
0.6423 Remote Similarity NPC315783
0.6423 Remote Similarity NPC314629
0.6415 Remote Similarity NPC110072
0.6415 Remote Similarity NPC270005
0.6415 Remote Similarity NPC208537
0.641 Remote Similarity NPC295444
0.641 Remote Similarity NPC279383
0.641 Remote Similarity NPC268327
0.641 Remote Similarity NPC273215
0.6408 Remote Similarity NPC477387
0.6408 Remote Similarity NPC477389
0.64 Remote Similarity NPC82799
0.6396 Remote Similarity NPC471637
0.6396 Remote Similarity NPC475157
0.6396 Remote Similarity NPC2313
0.6396 Remote Similarity NPC57586
0.6396 Remote Similarity NPC475655
0.6396 Remote Similarity NPC154132
0.6389 Remote Similarity NPC205546
0.6389 Remote Similarity NPC50902
0.6389 Remote Similarity NPC233273
0.6387 Remote Similarity NPC30196
0.6381 Remote Similarity NPC309310
0.6374 Remote Similarity NPC147292
0.6373 Remote Similarity NPC475035
0.6373 Remote Similarity NPC136699
0.6373 Remote Similarity NPC220167
0.6373 Remote Similarity NPC266718
0.6371 Remote Similarity NPC204639
0.6371 Remote Similarity NPC469494
0.6355 Remote Similarity NPC320089
0.6354 Remote Similarity NPC24590
0.6346 Remote Similarity NPC475037
0.6346 Remote Similarity NPC477386
0.6346 Remote Similarity NPC477388
0.6341 Remote Similarity NPC273185
0.6337 Remote Similarity NPC20072
0.6336 Remote Similarity NPC230889
0.6321 Remote Similarity NPC118078
0.6316 Remote Similarity NPC472433
0.6316 Remote Similarity NPC315070
0.6311 Remote Similarity NPC470124
0.6306 Remote Similarity NPC64348
0.63 Remote Similarity NPC133226
0.63 Remote Similarity NPC470147
0.6299 Remote Similarity NPC313962
0.6299 Remote Similarity NPC316205
0.6299 Remote Similarity NPC315387
0.6296 Remote Similarity NPC294293
0.6296 Remote Similarity NPC470283
0.6293 Remote Similarity NPC473578
0.6292 Remote Similarity NPC155457
0.6286 Remote Similarity NPC137368
0.6286 Remote Similarity NPC476744
0.6286 Remote Similarity NPC248312
0.6283 Remote Similarity NPC197736
0.6277 Remote Similarity NPC280065
0.6277 Remote Similarity NPC45060
0.6273 Remote Similarity NPC240372
0.6271 Remote Similarity NPC261750
0.6271 Remote Similarity NPC1111
0.6264 Remote Similarity NPC235311
0.6264 Remote Similarity NPC253468
0.6262 Remote Similarity NPC302584

  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 NPC45313 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
0.9222 High Similarity NPD8522 Clinical (unspecified phase)
0.6964 Remote Similarity NPD6421 Discontinued
0.6881 Remote Similarity NPD1407 Approved
0.6842 Remote Similarity NPD6429 Approved
0.6842 Remote Similarity NPD6430 Approved
0.6777 Remote Similarity NPD8341 Approved
0.6777 Remote Similarity NPD8342 Approved
0.6777 Remote Similarity NPD8340 Approved
0.6777 Remote Similarity NPD8299 Approved
0.6585 Remote Similarity NPD8451 Approved
0.6555 Remote Similarity NPD7641 Discontinued
0.6532 Remote Similarity NPD8448 Approved
0.6529 Remote Similarity NPD8444 Approved
0.646 Remote Similarity NPD5357 Phase 1
0.6423 Remote Similarity NPD7830 Approved
0.6423 Remote Similarity NPD7829 Approved
0.6378 Remote Similarity NPD8390 Approved
0.6378 Remote Similarity NPD8391 Approved
0.6378 Remote Similarity NPD8392 Approved
0.6341 Remote Similarity NPD6436 Phase 3
0.6316 Remote Similarity NPD6640 Phase 3
0.627 Remote Similarity NPD8074 Phase 3
0.6216 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6198 Remote Similarity NPD7505 Discontinued
0.6182 Remote Similarity NPD7839 Suspended
0.6111 Remote Similarity NPD7983 Approved
0.6105 Remote Similarity NPD9445 Approved
0.6032 Remote Similarity NPD7642 Approved
0.6019 Remote Similarity NPD7838 Discovery
0.5938 Remote Similarity NPD8273 Phase 1
0.5935 Remote Similarity NPD7500 Approved
0.5935 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5926 Remote Similarity NPD3716 Discontinued
0.5917 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5897 Remote Similarity NPD4211 Phase 1
0.5893 Remote Similarity NPD6428 Approved
0.5888 Remote Similarity NPD4759 Clinical (unspecified phase)
0.582 Remote Similarity NPD3731 Phase 3
0.5806 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5804 Remote Similarity NPD5381 Approved
0.5804 Remote Similarity NPD5377 Approved
0.5804 Remote Similarity NPD5378 Approved
0.5748 Remote Similarity NPD8513 Phase 3
0.5748 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5748 Remote Similarity NPD8516 Approved
0.5748 Remote Similarity NPD8515 Approved
0.5748 Remote Similarity NPD8517 Approved
0.5727 Remote Similarity NPD3168 Discontinued
0.5727 Remote Similarity NPD46 Approved
0.5727 Remote Similarity NPD6698 Approved
0.5726 Remote Similarity NPD4830 Approved
0.5726 Remote Similarity NPD4832 Approved
0.5726 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5726 Remote Similarity NPD4831 Approved
0.5703 Remote Similarity NPD8080 Discontinued
0.5703 Remote Similarity NPD7623 Phase 3
0.5703 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8174 Phase 2
0.5656 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5649 Remote Similarity NPD7747 Phase 1
0.5649 Remote Similarity NPD7746 Phase 1
0.5639 Remote Similarity NPD6914 Discontinued
0.563 Remote Similarity NPD5376 Approved

  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