Structure

Physi-Chem Properties

Molecular Weight:  634.39
Volume:  645.125
LogP:  4.572
LogD:  3.574
LogS:  -3.818
# Rotatable Bonds:  23
TPSA:  170.44
# H-Bond Aceptor:  12
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.107
Synthetic Accessibility Score:  4.534
Fsp3:  0.938
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.078
MDCK Permeability:  1.4557055692421272e-05
Pgp-inhibitor:  0.994
Pgp-substrate:  0.939
Human Intestinal Absorption (HIA):  0.863
20% Bioavailability (F20%):  0.848
30% Bioavailability (F30%):  0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.014
Plasma Protein Binding (PPB):  97.01504516601562%
Volume Distribution (VD):  1.359
Pgp-substrate:  4.564438343048096%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.105
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.08
CYP2C9-substrate:  0.053
CYP2D6-inhibitor:  0.432
CYP2D6-substrate:  0.021
CYP3A4-inhibitor:  0.159
CYP3A4-substrate:  0.047

ADMET: Excretion

Clearance (CL):  1.441
Half-life (T1/2):  0.544

ADMET: Toxicity

hERG Blockers:  0.424
Human Hepatotoxicity (H-HT):  0.141
Drug-inuced Liver Injury (DILI):  0.571
AMES Toxicity:  0.181
Rat Oral Acute Toxicity:  0.018
Maximum Recommended Daily Dose:  0.001
Skin Sensitization:  0.915
Carcinogencity:  0.071
Eye Corrosion:  0.007
Eye Irritation:  0.062
Respiratory Toxicity:  0.877

Download Data

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

  Natural Product: NPC471761

Natural Product ID:  NPC471761
Common Name*:   Hexadecyl-[O-3,4-Di-O-Acetyl-Alpha-L-Rhamnopyranosyl-(1->2)]-Beta-D-Glucopyranoside
IUPAC Name:   [(2S,3S,4S,5R,6S)-4-acetyloxy-6-[(2R,3R,4S,5S,6R)-2-hexadecoxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]oxy-5-hydroxy-2-methyloxan-3-yl] acetate
Synonyms:  
Standard InCHIKey:  FNGKSOSQXAAYSF-ZYLDGILESA-N
Standard InCHI:  InChI=1S/C32H58O12/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-39-32-30(26(37)25(36)24(20-33)43-32)44-31-27(38)29(42-23(4)35)28(21(2)40-31)41-22(3)34/h21,24-33,36-38H,5-20H2,1-4H3/t21-,24+,25+,26-,27+,28-,29-,30+,31-,32+/m0/s1
SMILES:  CCCCCCCCCCCCCCCCOC1C(C(C(C(O1)CO)O)O)OC2C(C(C(C(O2)C)OC(=O)C)OC(=O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3120542
PubChem CID:   76325281
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
NPO33220 matayba guianensis aublet Species Sapindaceae Eukaryota n.a. n.a. n.a. PMID[24485783]

☑ 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
NPT927 Cell Line PBMC Homo sapiens IC50 > 39430.0 nM PMID[506693]
NPT2 Others Unspecified Selectivity Index = 12.5 n.a. PMID[506693]
NPT188 Organism Candida parapsilosis Candida parapsilosis MIC = 3150.0 nM PMID[506693]

☑ 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 NPC471761 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 NPC471760
1.0 High Similarity NPC190418
0.9524 High Similarity NPC67099
0.9375 High Similarity NPC211428
0.9333 High Similarity NPC477750
0.9333 High Similarity NPC477762
0.9333 High Similarity NPC477753
0.9333 High Similarity NPC477763
0.9333 High Similarity NPC477757
0.9333 High Similarity NPC477755
0.9231 High Similarity NPC53760
0.9231 High Similarity NPC52268
0.9219 High Similarity NPC50228
0.9219 High Similarity NPC97736
0.9077 High Similarity NPC285003
0.9077 High Similarity NPC241265
0.8955 High Similarity NPC169085
0.8955 High Similarity NPC225748
0.8955 High Similarity NPC206823
0.8955 High Similarity NPC9763
0.8955 High Similarity NPC39266
0.8833 High Similarity NPC472025
0.8769 High Similarity NPC206601
0.875 High Similarity NPC12040
0.875 High Similarity NPC76881
0.8676 High Similarity NPC163812
0.8667 High Similarity NPC148424
0.8615 High Similarity NPC477756
0.8615 High Similarity NPC477751
0.8615 High Similarity NPC477764
0.8615 High Similarity NPC477752
0.8571 High Similarity NPC477350
0.8485 Intermediate Similarity NPC477760
0.8485 Intermediate Similarity NPC477759
0.8485 Intermediate Similarity NPC477758
0.8485 Intermediate Similarity NPC477754
0.8485 Intermediate Similarity NPC477761
0.8451 Intermediate Similarity NPC476783
0.8451 Intermediate Similarity NPC476782
0.8451 Intermediate Similarity NPC216883
0.8451 Intermediate Similarity NPC476781
0.8406 Intermediate Similarity NPC291228
0.8406 Intermediate Similarity NPC308096
0.8358 Intermediate Similarity NPC250619
0.8333 Intermediate Similarity NPC477330
0.8333 Intermediate Similarity NPC303727
0.8333 Intermediate Similarity NPC477328
0.8333 Intermediate Similarity NPC475425
0.8333 Intermediate Similarity NPC477325
0.8333 Intermediate Similarity NPC477326
0.8333 Intermediate Similarity NPC113745
0.8333 Intermediate Similarity NPC477320
0.8333 Intermediate Similarity NPC281563
0.8333 Intermediate Similarity NPC146380
0.8333 Intermediate Similarity NPC477329
0.8333 Intermediate Similarity NPC109887
0.8333 Intermediate Similarity NPC477323
0.8261 Intermediate Similarity NPC184550
0.8261 Intermediate Similarity NPC185419
0.8219 Intermediate Similarity NPC158302
0.8219 Intermediate Similarity NPC294748
0.8219 Intermediate Similarity NPC146992
0.8219 Intermediate Similarity NPC85759
0.8219 Intermediate Similarity NPC22742
0.8219 Intermediate Similarity NPC477346
0.8219 Intermediate Similarity NPC477344
0.8167 Intermediate Similarity NPC145112
0.8167 Intermediate Similarity NPC58629
0.8167 Intermediate Similarity NPC67660
0.8167 Intermediate Similarity NPC107914
0.8167 Intermediate Similarity NPC157514
0.8167 Intermediate Similarity NPC165198
0.8167 Intermediate Similarity NPC89145
0.8167 Intermediate Similarity NPC269166
0.8167 Intermediate Similarity NPC246558
0.8167 Intermediate Similarity NPC242073
0.8154 Intermediate Similarity NPC325773
0.8108 Intermediate Similarity NPC267592
0.8095 Intermediate Similarity NPC320032
0.8095 Intermediate Similarity NPC34877
0.8095 Intermediate Similarity NPC290179
0.8095 Intermediate Similarity NPC317023
0.8 Intermediate Similarity NPC477331
0.8 Intermediate Similarity NPC476087
0.8 Intermediate Similarity NPC123204
0.8 Intermediate Similarity NPC475667
0.8 Intermediate Similarity NPC472204
0.8 Intermediate Similarity NPC269318
0.8 Intermediate Similarity NPC224953
0.8 Intermediate Similarity NPC472201
0.8 Intermediate Similarity NPC472202
0.8 Intermediate Similarity NPC297768
0.8 Intermediate Similarity NPC183888
0.8 Intermediate Similarity NPC115013
0.8 Intermediate Similarity NPC186992
0.8 Intermediate Similarity NPC307400
0.8 Intermediate Similarity NPC475270
0.8 Intermediate Similarity NPC143421
0.8 Intermediate Similarity NPC27289
0.8 Intermediate Similarity NPC477317
0.8 Intermediate Similarity NPC477318
0.8 Intermediate Similarity NPC259294
0.8 Intermediate Similarity NPC184915
0.8 Intermediate Similarity NPC119583
0.8 Intermediate Similarity NPC475327
0.8 Intermediate Similarity NPC477319
0.8 Intermediate Similarity NPC290012
0.8 Intermediate Similarity NPC472200
0.8 Intermediate Similarity NPC238056
0.8 Intermediate Similarity NPC173328
0.8 Intermediate Similarity NPC169345
0.8 Intermediate Similarity NPC477347
0.8 Intermediate Similarity NPC126685
0.8 Intermediate Similarity NPC472203
0.8 Intermediate Similarity NPC44782
0.8 Intermediate Similarity NPC472205
0.8 Intermediate Similarity NPC89843
0.7846 Intermediate Similarity NPC472026
0.7833 Intermediate Similarity NPC124963
0.7833 Intermediate Similarity NPC326533
0.7833 Intermediate Similarity NPC233726
0.7833 Intermediate Similarity NPC23134
0.7792 Intermediate Similarity NPC60849
0.7792 Intermediate Similarity NPC470313
0.7792 Intermediate Similarity NPC473500
0.7792 Intermediate Similarity NPC38295
0.7792 Intermediate Similarity NPC156089
0.7792 Intermediate Similarity NPC472352
0.7792 Intermediate Similarity NPC477332
0.7761 Intermediate Similarity NPC6848
0.7639 Intermediate Similarity NPC55652
0.7612 Intermediate Similarity NPC268243
0.7581 Intermediate Similarity NPC130683
0.7581 Intermediate Similarity NPC323361
0.7538 Intermediate Similarity NPC322855
0.7532 Intermediate Similarity NPC21693
0.7532 Intermediate Similarity NPC236649
0.75 Intermediate Similarity NPC157193
0.75 Intermediate Similarity NPC42503
0.75 Intermediate Similarity NPC282143
0.75 Intermediate Similarity NPC299781
0.7403 Intermediate Similarity NPC163362
0.7403 Intermediate Similarity NPC127295
0.7391 Intermediate Similarity NPC147292
0.7385 Intermediate Similarity NPC219040
0.7361 Intermediate Similarity NPC474078
0.7333 Intermediate Similarity NPC14144
0.7297 Intermediate Similarity NPC138273
0.7237 Intermediate Similarity NPC110813
0.7188 Intermediate Similarity NPC289979
0.7183 Intermediate Similarity NPC32148
0.7167 Intermediate Similarity NPC277475
0.7167 Intermediate Similarity NPC321087
0.716 Intermediate Similarity NPC83839
0.7143 Intermediate Similarity NPC133377
0.7123 Intermediate Similarity NPC471879
0.7105 Intermediate Similarity NPC279575
0.7097 Intermediate Similarity NPC323574
0.7089 Intermediate Similarity NPC216941
0.7089 Intermediate Similarity NPC469469
0.7073 Intermediate Similarity NPC470657
0.7067 Intermediate Similarity NPC308489
0.7067 Intermediate Similarity NPC166250
0.7059 Intermediate Similarity NPC477349
0.7037 Intermediate Similarity NPC288471
0.7013 Intermediate Similarity NPC244002
0.7 Intermediate Similarity NPC255377
0.7 Intermediate Similarity NPC73906
0.7 Intermediate Similarity NPC92246
0.7 Intermediate Similarity NPC21209
0.7 Intermediate Similarity NPC165846
0.7 Intermediate Similarity NPC289758
0.7 Intermediate Similarity NPC69445
0.7 Intermediate Similarity NPC176017
0.7 Intermediate Similarity NPC475849
0.7 Intermediate Similarity NPC199857
0.7 Intermediate Similarity NPC285364
0.6988 Remote Similarity NPC31349
0.6988 Remote Similarity NPC314364
0.6988 Remote Similarity NPC51662
0.6935 Remote Similarity NPC82512
0.6923 Remote Similarity NPC272841
0.6923 Remote Similarity NPC53463
0.6923 Remote Similarity NPC320588
0.6923 Remote Similarity NPC469937
0.6923 Remote Similarity NPC23155
0.6914 Remote Similarity NPC474266
0.6912 Remote Similarity NPC143326
0.6897 Remote Similarity NPC477345
0.6897 Remote Similarity NPC44682
0.6897 Remote Similarity NPC470283
0.6897 Remote Similarity NPC477348
0.6897 Remote Similarity NPC163409
0.6897 Remote Similarity NPC238264
0.6867 Remote Similarity NPC471410
0.6867 Remote Similarity NPC471411
0.6867 Remote Similarity NPC208473
0.6857 Remote Similarity NPC277570
0.6835 Remote Similarity NPC170595
0.6829 Remote Similarity NPC253975

  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 NPC471761 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
0.8167 Intermediate Similarity NPD891 Phase 3
0.8167 Intermediate Similarity NPD893 Approved
0.8167 Intermediate Similarity NPD890 Clinical (unspecified phase)
0.8167 Intermediate Similarity NPD892 Phase 3
0.8167 Intermediate Similarity NPD888 Phase 3
0.8 Intermediate Similarity NPD2269 Approved
0.7846 Intermediate Similarity NPD6123 Approved
0.7833 Intermediate Similarity NPD904 Phase 3
0.7833 Intermediate Similarity NPD905 Approved
0.7581 Intermediate Similarity NPD889 Approved
0.7581 Intermediate Similarity NPD894 Approved
0.7581 Intermediate Similarity NPD887 Approved
0.7581 Intermediate Similarity NPD895 Approved
0.75 Intermediate Similarity NPD2267 Suspended
0.746 Intermediate Similarity NPD7346 Approved
0.7273 Intermediate Similarity NPD7329 Approved
0.7183 Intermediate Similarity NPD898 Approved
0.7183 Intermediate Similarity NPD896 Approved
0.7183 Intermediate Similarity NPD897 Approved
0.7162 Intermediate Similarity NPD3181 Approved
0.7123 Intermediate Similarity NPD7532 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD8997 Approved
0.7 Intermediate Similarity NPD8998 Phase 2
0.7 Intermediate Similarity NPD8999 Phase 3
0.7 Intermediate Similarity NPD8993 Phase 1
0.7 Intermediate Similarity NPD9000 Phase 3
0.6923 Remote Similarity NPD3728 Approved
0.6923 Remote Similarity NPD3730 Approved
0.6866 Remote Similarity NPD369 Approved
0.6774 Remote Similarity NPD8966 Approved
0.6774 Remote Similarity NPD8965 Approved
0.662 Remote Similarity NPD847 Phase 1
0.6515 Remote Similarity NPD9036 Phase 3
0.6515 Remote Similarity NPD9035 Clinical (unspecified phase)
0.6506 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6506 Remote Similarity NPD3669 Approved
0.65 Remote Similarity NPD8788 Approved
0.6462 Remote Similarity NPD1400 Approved
0.6462 Remote Similarity NPD1399 Approved
0.6389 Remote Similarity NPD8961 Approved
0.6383 Remote Similarity NPD8082 Approved
0.6383 Remote Similarity NPD8138 Approved
0.6383 Remote Similarity NPD8083 Approved
0.6383 Remote Similarity NPD8085 Approved
0.6383 Remote Similarity NPD8139 Approved
0.6383 Remote Similarity NPD8086 Approved
0.6383 Remote Similarity NPD8084 Approved
0.6316 Remote Similarity NPD8275 Approved
0.6316 Remote Similarity NPD8276 Approved
0.625 Remote Similarity NPD8081 Approved
0.6222 Remote Similarity NPD8171 Discontinued
0.6203 Remote Similarity NPD1811 Approved
0.6203 Remote Similarity NPD1810 Approved
0.6186 Remote Similarity NPD8393 Approved
0.6167 Remote Similarity NPD7536 Approved
0.6129 Remote Similarity NPD9006 Approved
0.6122 Remote Similarity NPD8307 Discontinued
0.6122 Remote Similarity NPD8140 Approved
0.6081 Remote Similarity NPD1457 Discontinued
0.6022 Remote Similarity NPD6428 Approved
0.6 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6 Remote Similarity NPD8306 Approved
0.6 Remote Similarity NPD8305 Approved
0.6 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5941 Remote Similarity NPD8087 Discontinued
0.5918 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5915 Remote Similarity NPD8959 Approved
0.5895 Remote Similarity NPD8029 Clinical (unspecified phase)
0.587 Remote Similarity NPD1446 Phase 3
0.587 Remote Similarity NPD1447 Phase 3
0.5867 Remote Similarity NPD7909 Approved
0.5857 Remote Similarity NPD885 Approved
0.5857 Remote Similarity NPD884 Clinical (unspecified phase)
0.5842 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5842 Remote Similarity NPD6941 Approved
0.5823 Remote Similarity NPD2686 Approved
0.5823 Remote Similarity NPD2687 Approved
0.5823 Remote Similarity NPD2254 Approved
0.5816 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5781 Remote Similarity NPD9219 Approved
0.5781 Remote Similarity NPD9218 Clinical (unspecified phase)
0.5769 Remote Similarity NPD8133 Approved
0.5743 Remote Similarity NPD6686 Approved
0.573 Remote Similarity NPD3200 Clinical (unspecified phase)
0.5729 Remote Similarity NPD2255 Approved
0.5714 Remote Similarity NPD7140 Approved
0.5714 Remote Similarity NPD7139 Approved
0.5714 Remote Similarity NPD3716 Discontinued
0.5714 Remote Similarity NPD7141 Clinical (unspecified phase)
0.5698 Remote Similarity NPD1779 Approved
0.5698 Remote Similarity NPD1780 Approved
0.5692 Remote Similarity NPD8994 Approved
0.5667 Remote Similarity NPD3207 Approved
0.5667 Remote Similarity NPD3203 Approved
0.5667 Remote Similarity NPD3201 Approved
0.5667 Remote Similarity NPD3208 Approved
0.5667 Remote Similarity NPD3202 Approved
0.5667 Remote Similarity NPD4759 Clinical (unspecified phase)
0.5667 Remote Similarity NPD3209 Approved
0.5658 Remote Similarity NPD371 Approved
0.5652 Remote Similarity NPD6698 Approved
0.5652 Remote Similarity NPD9050 Approved
0.5652 Remote Similarity NPD46 Approved
0.5652 Remote Similarity NPD9049 Discontinued
0.5632 Remote Similarity NPD882 Phase 2
0.5632 Remote Similarity NPD883 Phase 2
0.5607 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5607 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5604 Remote Similarity NPD618 Clinical (unspecified phase)

  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