Structure

Physi-Chem Properties

Molecular Weight:  938.47
Volume:  909.403
LogP:  3.856
LogD:  2.804
LogS:  -4.491
# Rotatable Bonds:  26
TPSA:  280.19
# H-Bond Aceptor:  21
# H-Bond Donor:  5
# Rings:  4
# Heavy Atoms:  21

MedChem Properties

QED Drug-Likeness Score:  0.059
Synthetic Accessibility Score:  5.706
Fsp3:  0.909
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:  -5.274
MDCK Permeability:  0.00023035236517898738
Pgp-inhibitor:  0.987
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.978
20% Bioavailability (F20%):  0.0
30% Bioavailability (F30%):  0.874

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.01
Plasma Protein Binding (PPB):  80.2779769897461%
Volume Distribution (VD):  0.889
Pgp-substrate:  8.824026107788086%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.057
CYP2C19-inhibitor:  0.006
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.004
CYP2D6-inhibitor:  0.767
CYP2D6-substrate:  0.015
CYP3A4-inhibitor:  0.124
CYP3A4-substrate:  0.04

ADMET: Excretion

Clearance (CL):  1.042
Half-life (T1/2):  0.773

ADMET: Toxicity

hERG Blockers:  0.674
Human Hepatotoxicity (H-HT):  0.749
Drug-inuced Liver Injury (DILI):  0.968
AMES Toxicity:  0.102
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.001
Skin Sensitization:  0.906
Carcinogencity:  0.062
Eye Corrosion:  0.004
Eye Irritation:  0.009
Respiratory Toxicity:  0.882

Download Data

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

  Natural Product: NPC53760

Natural Product ID:  NPC53760
Common Name*:   1-O-Dodecanyl-3-O-Acetyl-Alpha-Rhamnopyranosyl-(1->3)-2,4-Di-O-Acetyl-Alpha-Rhamnopyranosyl-(1->3)-4-O-Acetyl-Alpha-Rhamnopyranosyl-(1->4)-Alpha-Rhamnopyranoside
IUPAC Name:   [(2S,3S,4S,5R,6S)-4-[(2S,3R,4R,5S,6S)-3,5-diacetyloxy-4-[(2S,3R,4R,5S,6S)-4-acetyloxy-3,5-dihydroxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-6-[(2S,3R,4S,5R,6R)-6-dodecoxy-4,5-dihydroxy-2-methyloxan-3-yl]oxy-5-hydroxy-2-methyloxan-3-yl] acetate
Synonyms:   Cleistetroside-8
Standard InCHIKey:  DBKWNJBMILFUAO-WOUDXDDQSA-N
Standard InCHI:  InChI=1S/C44H74O21/c1-10-11-12-13-14-15-16-17-18-19-20-54-41-31(51)30(50)34(22(3)56-41)63-43-33(53)38(35(23(4)57-43)59-25(6)45)64-44-40(62-28(9)48)39(36(24(5)58-44)60-26(7)46)65-42-32(52)37(61-27(8)47)29(49)21(2)55-42/h21-24,29-44,49-53H,10-20H2,1-9H3/t21-,22-,23-,24-,29-,30-,31+,32+,33+,34-,35-,36-,37+,38-,39+,40+,41+,42-,43-,44-/m0/s1
SMILES:  CCCCCCCCCCCCO[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1OC(=O)C)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)OC(=O)C)O)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509094
PubChem CID:   11636552
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

*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
NPO27352 Cleistopholis patens Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[16643031]
NPO27352 Cleistopholis patens Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[3325614]
NPO27352 Cleistopholis patens Species Annonaceae 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 8.0 ug.mL-1 PMID[448453]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 16.0 ug.mL-1 PMID[448453]

☑ 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 NPC53760 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 NPC52268
0.9692 High Similarity NPC67099
0.9286 High Similarity NPC477350
0.9231 High Similarity NPC471761
0.9231 High Similarity NPC190418
0.9231 High Similarity NPC471760
0.9155 High Similarity NPC476782
0.9155 High Similarity NPC216883
0.9155 High Similarity NPC476783
0.9155 High Similarity NPC476781
0.913 High Similarity NPC169085
0.913 High Similarity NPC225748
0.913 High Similarity NPC9763
0.913 High Similarity NPC39266
0.9028 High Similarity NPC477329
0.9028 High Similarity NPC281563
0.9028 High Similarity NPC477320
0.9028 High Similarity NPC477325
0.9028 High Similarity NPC477323
0.9028 High Similarity NPC109887
0.9028 High Similarity NPC477326
0.9028 High Similarity NPC113745
0.9028 High Similarity NPC477330
0.9028 High Similarity NPC477328
0.9028 High Similarity NPC475425
0.9028 High Similarity NPC146380
0.8904 High Similarity NPC22742
0.8904 High Similarity NPC477344
0.8904 High Similarity NPC158302
0.8904 High Similarity NPC85759
0.8904 High Similarity NPC477346
0.8904 High Similarity NPC294748
0.8904 High Similarity NPC146992
0.8857 High Similarity NPC206823
0.8857 High Similarity NPC163812
0.8784 High Similarity NPC267592
0.8696 High Similarity NPC211428
0.8667 High Similarity NPC472203
0.8667 High Similarity NPC119583
0.8667 High Similarity NPC238056
0.8667 High Similarity NPC475270
0.8667 High Similarity NPC476087
0.8667 High Similarity NPC477319
0.8667 High Similarity NPC307400
0.8667 High Similarity NPC290012
0.8667 High Similarity NPC477317
0.8667 High Similarity NPC472201
0.8667 High Similarity NPC123204
0.8667 High Similarity NPC89843
0.8667 High Similarity NPC475667
0.8667 High Similarity NPC472204
0.8667 High Similarity NPC472202
0.8667 High Similarity NPC126685
0.8667 High Similarity NPC259294
0.8667 High Similarity NPC477347
0.8667 High Similarity NPC472200
0.8667 High Similarity NPC475327
0.8667 High Similarity NPC186992
0.8667 High Similarity NPC169345
0.8667 High Similarity NPC173328
0.8667 High Similarity NPC477331
0.8667 High Similarity NPC477318
0.8667 High Similarity NPC44782
0.8667 High Similarity NPC297768
0.8667 High Similarity NPC184915
0.8667 High Similarity NPC269318
0.8667 High Similarity NPC224953
0.8667 High Similarity NPC143421
0.8667 High Similarity NPC472205
0.8667 High Similarity NPC115013
0.8667 High Similarity NPC183888
0.8667 High Similarity NPC27289
0.8615 High Similarity NPC477753
0.8615 High Similarity NPC477762
0.8615 High Similarity NPC477755
0.8615 High Similarity NPC477750
0.8615 High Similarity NPC477763
0.8615 High Similarity NPC477757
0.8551 High Similarity NPC97736
0.8551 High Similarity NPC50228
0.8551 High Similarity NPC250619
0.8507 High Similarity NPC6848
0.8442 Intermediate Similarity NPC477332
0.8442 Intermediate Similarity NPC472352
0.8442 Intermediate Similarity NPC60849
0.8429 Intermediate Similarity NPC285003
0.8429 Intermediate Similarity NPC241265
0.8308 Intermediate Similarity NPC317023
0.8154 Intermediate Similarity NPC472025
0.8143 Intermediate Similarity NPC206601
0.8116 Intermediate Similarity NPC76881
0.8116 Intermediate Similarity NPC12040
0.8 Intermediate Similarity NPC477764
0.8 Intermediate Similarity NPC477752
0.8 Intermediate Similarity NPC477751
0.8 Intermediate Similarity NPC148424
0.8 Intermediate Similarity NPC477756
0.7887 Intermediate Similarity NPC477758
0.7887 Intermediate Similarity NPC477754
0.7887 Intermediate Similarity NPC477761
0.7887 Intermediate Similarity NPC477760
0.7887 Intermediate Similarity NPC477759
0.7838 Intermediate Similarity NPC291228
0.7838 Intermediate Similarity NPC308096
0.7761 Intermediate Similarity NPC34877
0.7761 Intermediate Similarity NPC290179
0.7703 Intermediate Similarity NPC185419
0.7703 Intermediate Similarity NPC184550
0.7692 Intermediate Similarity NPC303727
0.7647 Intermediate Similarity NPC477349
0.7571 Intermediate Similarity NPC325773
0.7538 Intermediate Similarity NPC58629
0.7538 Intermediate Similarity NPC67660
0.7538 Intermediate Similarity NPC89145
0.7538 Intermediate Similarity NPC145112
0.7538 Intermediate Similarity NPC157514
0.7538 Intermediate Similarity NPC107914
0.7538 Intermediate Similarity NPC246558
0.7538 Intermediate Similarity NPC165198
0.7538 Intermediate Similarity NPC242073
0.7538 Intermediate Similarity NPC269166
0.75 Intermediate Similarity NPC320032
0.7471 Intermediate Similarity NPC477348
0.7471 Intermediate Similarity NPC477345
0.7471 Intermediate Similarity NPC238264
0.7471 Intermediate Similarity NPC163409
0.7471 Intermediate Similarity NPC44682
0.7407 Intermediate Similarity NPC248415
0.7317 Intermediate Similarity NPC473500
0.7317 Intermediate Similarity NPC38295
0.7317 Intermediate Similarity NPC156089
0.7317 Intermediate Similarity NPC470313
0.7303 Intermediate Similarity NPC475241
0.7303 Intermediate Similarity NPC473765
0.7303 Intermediate Similarity NPC476066
0.7303 Intermediate Similarity NPC473605
0.7303 Intermediate Similarity NPC475525
0.7303 Intermediate Similarity NPC475164
0.7303 Intermediate Similarity NPC475540
0.7303 Intermediate Similarity NPC475375
0.7303 Intermediate Similarity NPC475593
0.7286 Intermediate Similarity NPC472026
0.7231 Intermediate Similarity NPC326533
0.7231 Intermediate Similarity NPC124963
0.7231 Intermediate Similarity NPC233726
0.7231 Intermediate Similarity NPC23134
0.7143 Intermediate Similarity NPC209798
0.7143 Intermediate Similarity NPC471375
0.7143 Intermediate Similarity NPC55652
0.7143 Intermediate Similarity NPC471374
0.7083 Intermediate Similarity NPC268243
0.7073 Intermediate Similarity NPC21693
0.7073 Intermediate Similarity NPC236649
0.7065 Intermediate Similarity NPC471428
0.7065 Intermediate Similarity NPC471427
0.7065 Intermediate Similarity NPC471426
0.7065 Intermediate Similarity NPC51579
0.7045 Intermediate Similarity NPC110072
0.7033 Intermediate Similarity NPC210157
0.7033 Intermediate Similarity NPC470591
0.7015 Intermediate Similarity NPC323361
0.7015 Intermediate Similarity NPC130683
0.7 Intermediate Similarity NPC322855
0.7 Intermediate Similarity NPC244002
0.6989 Remote Similarity NPC154132
0.6989 Remote Similarity NPC2313
0.6989 Remote Similarity NPC475655
0.6989 Remote Similarity NPC57586
0.6989 Remote Similarity NPC471637
0.6989 Remote Similarity NPC475157
0.6977 Remote Similarity NPC51662
0.6951 Remote Similarity NPC127295
0.6951 Remote Similarity NPC163362
0.6923 Remote Similarity NPC157193
0.6923 Remote Similarity NPC42503
0.6923 Remote Similarity NPC299781
0.6923 Remote Similarity NPC282143
0.6892 Remote Similarity NPC147292
0.6883 Remote Similarity NPC474078
0.6857 Remote Similarity NPC219040
0.6835 Remote Similarity NPC138273
0.6818 Remote Similarity NPC285588
0.6813 Remote Similarity NPC94582
0.6813 Remote Similarity NPC57964
0.679 Remote Similarity NPC110813
0.6769 Remote Similarity NPC14144
0.6744 Remote Similarity NPC83839
0.6739 Remote Similarity NPC237071
0.6739 Remote Similarity NPC296936
0.6739 Remote Similarity NPC203434
0.6739 Remote Similarity NPC238796
0.6711 Remote Similarity NPC32148
0.6707 Remote Similarity NPC133377
0.6703 Remote Similarity NPC470283
0.6703 Remote Similarity NPC191915
0.6703 Remote Similarity NPC267238
0.6703 Remote Similarity NPC77717
0.6703 Remote Similarity NPC253611
0.6703 Remote Similarity NPC471373
0.6703 Remote Similarity NPC151214

  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 NPC53760 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
0.8615 High Similarity NPD6123 Approved
0.7922 Intermediate Similarity NPD7329 Approved
0.7692 Intermediate Similarity NPD7346 Approved
0.7538 Intermediate Similarity NPD890 Clinical (unspecified phase)
0.7538 Intermediate Similarity NPD892 Phase 3
0.7538 Intermediate Similarity NPD893 Approved
0.7538 Intermediate Similarity NPD891 Phase 3
0.7538 Intermediate Similarity NPD888 Phase 3
0.7385 Intermediate Similarity NPD2269 Approved
0.7231 Intermediate Similarity NPD904 Phase 3
0.7231 Intermediate Similarity NPD905 Approved
0.7015 Intermediate Similarity NPD895 Approved
0.7015 Intermediate Similarity NPD894 Approved
0.7015 Intermediate Similarity NPD887 Approved
0.7015 Intermediate Similarity NPD889 Approved
0.6957 Remote Similarity NPD2267 Suspended
0.6923 Remote Similarity NPD3181 Approved
0.6711 Remote Similarity NPD897 Approved
0.6711 Remote Similarity NPD896 Approved
0.6711 Remote Similarity NPD898 Approved
0.6667 Remote Similarity NPD7532 Clinical (unspecified phase)
0.662 Remote Similarity NPD369 Approved
0.6462 Remote Similarity NPD8999 Phase 3
0.6462 Remote Similarity NPD8993 Phase 1
0.6462 Remote Similarity NPD9000 Phase 3
0.6462 Remote Similarity NPD8998 Phase 2
0.6462 Remote Similarity NPD8997 Approved
0.6429 Remote Similarity NPD3730 Approved
0.6429 Remote Similarity NPD3728 Approved
0.6413 Remote Similarity NPD8171 Discontinued
0.6322 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6322 Remote Similarity NPD3669 Approved
0.6269 Remote Similarity NPD8966 Approved
0.6269 Remote Similarity NPD8965 Approved
0.6224 Remote Similarity NPD7141 Clinical (unspecified phase)
0.6224 Remote Similarity NPD7139 Approved
0.6224 Remote Similarity NPD7140 Approved
0.6184 Remote Similarity NPD847 Phase 1
0.61 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6095 Remote Similarity NPD8133 Approved
0.6061 Remote Similarity NPD8083 Approved
0.6061 Remote Similarity NPD8082 Approved
0.6061 Remote Similarity NPD8086 Approved
0.6061 Remote Similarity NPD8138 Approved
0.6061 Remote Similarity NPD8085 Approved
0.6061 Remote Similarity NPD8084 Approved
0.6061 Remote Similarity NPD8139 Approved
0.6056 Remote Similarity NPD9035 Clinical (unspecified phase)
0.6056 Remote Similarity NPD9036 Phase 3
0.604 Remote Similarity NPD8393 Approved
0.6024 Remote Similarity NPD1811 Approved
0.6024 Remote Similarity NPD1810 Approved
0.6 Remote Similarity NPD8788 Approved
0.6 Remote Similarity NPD1399 Approved
0.6 Remote Similarity NPD1400 Approved
0.6 Remote Similarity NPD8275 Approved
0.6 Remote Similarity NPD8276 Approved
0.5974 Remote Similarity NPD8961 Approved
0.5941 Remote Similarity NPD8081 Approved
0.5905 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5865 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5825 Remote Similarity NPD8307 Discontinued
0.5825 Remote Similarity NPD8140 Approved
0.5714 Remote Similarity NPD8516 Approved
0.5714 Remote Similarity NPD8305 Approved
0.5714 Remote Similarity NPD6941 Approved
0.5714 Remote Similarity NPD6428 Approved
0.5714 Remote Similarity NPD8515 Approved
0.5714 Remote Similarity NPD8306 Approved
0.5714 Remote Similarity NPD8517 Approved
0.5696 Remote Similarity NPD1457 Discontinued
0.5696 Remote Similarity NPD7909 Approved
0.5692 Remote Similarity NPD7536 Approved
0.5686 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5684 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5672 Remote Similarity NPD9006 Approved
0.5663 Remote Similarity NPD2254 Approved
0.5663 Remote Similarity NPD2686 Approved
0.5663 Remote Similarity NPD2687 Approved
0.566 Remote Similarity NPD8087 Discontinued
0.5636 Remote Similarity NPD8295 Clinical (unspecified phase)
0.5625 Remote Similarity NPD8377 Approved
0.5625 Remote Similarity NPD8294 Approved
0.5619 Remote Similarity NPD6686 Approved
0.56 Remote Similarity NPD8029 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