Structure

Physi-Chem Properties

Molecular Weight:  1026.56
Volume:  1007.31
LogP:  3.666
LogD:  3.119
LogS:  -3.5
# Rotatable Bonds:  32
TPSA:  325.58
# H-Bond Aceptor:  22
# H-Bond Donor:  9
# Rings:  4
# Heavy Atoms:  22

MedChem Properties

QED Drug-Likeness Score:  0.036
Synthetic Accessibility Score:  6.121
Fsp3:  0.939
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:  -5.791
MDCK Permeability:  0.00011735133739421144
Pgp-inhibitor:  0.9
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.992
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.014
Plasma Protein Binding (PPB):  95.25672149658203%
Volume Distribution (VD):  0.322
Pgp-substrate:  7.80574893951416%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.035
CYP2C19-inhibitor:  0.006
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.027
CYP2D6-inhibitor:  0.107
CYP2D6-substrate:  0.021
CYP3A4-inhibitor:  0.045
CYP3A4-substrate:  0.009

ADMET: Excretion

Clearance (CL):  0.916
Half-life (T1/2):  0.771

ADMET: Toxicity

hERG Blockers:  0.802
Human Hepatotoxicity (H-HT):  0.64
Drug-inuced Liver Injury (DILI):  0.696
AMES Toxicity:  0.132
Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.001
Skin Sensitization:  0.46
Carcinogencity:  0.036
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.048

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

  Natural Product: NPC216883

Natural Product ID:  NPC216883
Common Name*:   Caminosides A
IUPAC Name:   [(2S,3R,4S,5R,6R)-5-acetyloxy-2-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[(10R)-2-oxononadecan-10-yl]oxyoxan-3-yl]oxy-3-[(2S,3S,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy-6-[[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxymethyl]oxan-4-yl] butanoate
Synonyms:  
Standard InCHIKey:  XTQWRNIJLVUYJY-ZFMPSFEPSA-N
Standard InCHI:  InChI=1S/C49H86O22/c1-7-9-10-11-12-15-18-22-30(23-19-16-13-14-17-21-26(3)51)66-48-43(39(59)36(56)31(24-50)67-48)70-49-45(71-47-41(61)38(58)35(55)28(5)64-47)44(69-33(53)20-8-2)42(65-29(6)52)32(68-49)25-62-46-40(60)37(57)34(54)27(4)63-46/h27-28,30-32,34-50,54-61H,7-25H2,1-6H3/t27-,28+,30-,31-,32-,34+,35+,36-,37+,38-,39+,40+,41+,42-,43-,44+,45-,46-,47+,48-,49+/m1/s1
SMILES:  CCCCCCCCC[C@H](CCCCCCCC(=O)C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@H]([C@H]([C@H]([C@@H](C)O2)O)O)O)O1)OC(=O)C)OC(=O)CCC)O[C@H]1[C@H]([C@@H]([C@H]([C@H](C)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL502428
PubChem CID:   21777925
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003918] Saccharolipids

*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
NPO27310 Caminus sphaeroconia Species Geodiidae Eukaryota n.a. n.a. n.a. PMID[12423093]
NPO27310 Caminus sphaeroconia Species Geodiidae Eukaryota n.a. at 10 m from Toucari Caves in Dominica, Netherlands n.a. PMID[16499312]
NPO27310 Caminus sphaeroconia Species Geodiidae 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 = 12.5 ug PMID[547091]
NPT1605 Organism Enterococcus Enterococcus MIC = 12.5 ug PMID[547091]
NPT1521 Organism Stenotrophomonas maltophilia Stenotrophomonas maltophilia MIC = 25.0 ug PMID[547091]
NPT2527 Organism Pythium ultimum Pythium ultimum MIC = 50.0 ug PMID[547091]
NPT19 Organism Escherichia coli Escherichia coli IC50 = 20000.0 nM PMID[547091]

☑ 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 NPC216883 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 NPC476782
1.0 High Similarity NPC476783
1.0 High Similarity NPC476781
0.9859 High Similarity NPC477350
0.9589 High Similarity NPC477320
0.9589 High Similarity NPC477325
0.9589 High Similarity NPC109887
0.9589 High Similarity NPC281563
0.9589 High Similarity NPC477323
0.9589 High Similarity NPC477329
0.9589 High Similarity NPC146380
0.9589 High Similarity NPC477330
0.9589 High Similarity NPC477326
0.9589 High Similarity NPC113745
0.9589 High Similarity NPC477328
0.9589 High Similarity NPC475425
0.9459 High Similarity NPC146992
0.9459 High Similarity NPC158302
0.9459 High Similarity NPC477346
0.9459 High Similarity NPC85759
0.9459 High Similarity NPC477344
0.9459 High Similarity NPC294748
0.9459 High Similarity NPC22742
0.9437 High Similarity NPC163812
0.9437 High Similarity NPC9763
0.9437 High Similarity NPC169085
0.9437 High Similarity NPC206823
0.9437 High Similarity NPC39266
0.9437 High Similarity NPC225748
0.9333 High Similarity NPC267592
0.9211 High Similarity NPC475667
0.9211 High Similarity NPC119583
0.9211 High Similarity NPC238056
0.9211 High Similarity NPC307400
0.9211 High Similarity NPC477331
0.9211 High Similarity NPC472205
0.9211 High Similarity NPC477347
0.9211 High Similarity NPC475327
0.9211 High Similarity NPC184915
0.9211 High Similarity NPC224953
0.9211 High Similarity NPC143421
0.9211 High Similarity NPC290012
0.9211 High Similarity NPC186992
0.9211 High Similarity NPC44782
0.9211 High Similarity NPC297768
0.9211 High Similarity NPC169345
0.9211 High Similarity NPC476087
0.9211 High Similarity NPC173328
0.9211 High Similarity NPC472200
0.9211 High Similarity NPC123204
0.9211 High Similarity NPC115013
0.9211 High Similarity NPC475270
0.9211 High Similarity NPC477317
0.9211 High Similarity NPC259294
0.9211 High Similarity NPC183888
0.9211 High Similarity NPC27289
0.9211 High Similarity NPC477318
0.9211 High Similarity NPC89843
0.9211 High Similarity NPC269318
0.9211 High Similarity NPC472202
0.9211 High Similarity NPC472203
0.9211 High Similarity NPC472204
0.9211 High Similarity NPC472201
0.9211 High Similarity NPC477319
0.9211 High Similarity NPC126685
0.9155 High Similarity NPC53760
0.9155 High Similarity NPC52268
0.9014 High Similarity NPC285003
0.9014 High Similarity NPC241265
0.9014 High Similarity NPC211428
0.8974 High Similarity NPC60849
0.8974 High Similarity NPC477332
0.8974 High Similarity NPC472352
0.8873 High Similarity NPC67099
0.8873 High Similarity NPC250619
0.8873 High Similarity NPC50228
0.8873 High Similarity NPC97736
0.8732 High Similarity NPC206601
0.8451 Intermediate Similarity NPC76881
0.8451 Intermediate Similarity NPC190418
0.8451 Intermediate Similarity NPC471761
0.8451 Intermediate Similarity NPC471760
0.8451 Intermediate Similarity NPC12040
0.84 Intermediate Similarity NPC291228
0.84 Intermediate Similarity NPC308096
0.8267 Intermediate Similarity NPC184550
0.8267 Intermediate Similarity NPC185419
0.8169 Intermediate Similarity NPC325773
0.814 Intermediate Similarity NPC477349
0.7955 Intermediate Similarity NPC238264
0.7955 Intermediate Similarity NPC163409
0.7955 Intermediate Similarity NPC477348
0.7955 Intermediate Similarity NPC44682
0.7955 Intermediate Similarity NPC477345
0.7927 Intermediate Similarity NPC248415
0.7887 Intermediate Similarity NPC477757
0.7887 Intermediate Similarity NPC477755
0.7887 Intermediate Similarity NPC477762
0.7887 Intermediate Similarity NPC477753
0.7887 Intermediate Similarity NPC477750
0.7887 Intermediate Similarity NPC477763
0.7831 Intermediate Similarity NPC156089
0.7831 Intermediate Similarity NPC473500
0.7831 Intermediate Similarity NPC38295
0.7831 Intermediate Similarity NPC470313
0.7808 Intermediate Similarity NPC6848
0.7778 Intermediate Similarity NPC473605
0.7778 Intermediate Similarity NPC475241
0.7778 Intermediate Similarity NPC475375
0.7778 Intermediate Similarity NPC475164
0.7778 Intermediate Similarity NPC473765
0.7778 Intermediate Similarity NPC476066
0.7778 Intermediate Similarity NPC475525
0.7778 Intermediate Similarity NPC475593
0.7778 Intermediate Similarity NPC475540
0.7606 Intermediate Similarity NPC317023
0.759 Intermediate Similarity NPC21693
0.759 Intermediate Similarity NPC236649
0.7471 Intermediate Similarity NPC51662
0.7465 Intermediate Similarity NPC472025
0.7368 Intermediate Similarity NPC477764
0.7368 Intermediate Similarity NPC477752
0.7368 Intermediate Similarity NPC477756
0.7368 Intermediate Similarity NPC477751
0.7361 Intermediate Similarity NPC322855
0.7324 Intermediate Similarity NPC148424
0.7273 Intermediate Similarity NPC477754
0.7273 Intermediate Similarity NPC477761
0.7273 Intermediate Similarity NPC477759
0.7273 Intermediate Similarity NPC477758
0.7273 Intermediate Similarity NPC477760
0.7241 Intermediate Similarity NPC83839
0.7159 Intermediate Similarity NPC470657
0.7126 Intermediate Similarity NPC125253
0.7126 Intermediate Similarity NPC253975
0.7126 Intermediate Similarity NPC192025
0.7126 Intermediate Similarity NPC288471
0.7123 Intermediate Similarity NPC34877
0.7123 Intermediate Similarity NPC290179
0.7123 Intermediate Similarity NPC320032
0.7108 Intermediate Similarity NPC110813
0.7079 Intermediate Similarity NPC314364
0.7079 Intermediate Similarity NPC31349
0.7071 Intermediate Similarity NPC126753
0.7051 Intermediate Similarity NPC32148
0.7042 Intermediate Similarity NPC53463
0.7042 Intermediate Similarity NPC469937
0.7042 Intermediate Similarity NPC320588
0.7042 Intermediate Similarity NPC23155
0.7042 Intermediate Similarity NPC303727
0.7041 Intermediate Similarity NPC469827
0.703 Intermediate Similarity NPC470622
0.7024 Intermediate Similarity NPC133377
0.701 Intermediate Similarity NPC80191
0.701 Intermediate Similarity NPC310031
0.7 Intermediate Similarity NPC207693
0.6974 Remote Similarity NPC268243
0.697 Remote Similarity NPC184805
0.697 Remote Similarity NPC273189
0.6931 Remote Similarity NPC22709
0.6931 Remote Similarity NPC469825
0.6915 Remote Similarity NPC215570
0.6907 Remote Similarity NPC42320
0.6907 Remote Similarity NPC188453
0.6907 Remote Similarity NPC476611
0.6905 Remote Similarity NPC474003
0.6901 Remote Similarity NPC246558
0.6901 Remote Similarity NPC89145
0.6901 Remote Similarity NPC58629
0.6901 Remote Similarity NPC242073
0.6901 Remote Similarity NPC157514
0.6901 Remote Similarity NPC145112
0.6901 Remote Similarity NPC67660
0.6901 Remote Similarity NPC269166
0.6901 Remote Similarity NPC107914
0.6901 Remote Similarity NPC165198
0.69 Remote Similarity NPC287269
0.69 Remote Similarity NPC471430
0.6882 Remote Similarity NPC320089
0.6869 Remote Similarity NPC231271
0.6869 Remote Similarity NPC470519
0.6869 Remote Similarity NPC267637
0.6863 Remote Similarity NPC471431
0.6842 Remote Similarity NPC143446
0.6832 Remote Similarity NPC92890
0.6832 Remote Similarity NPC469826
0.6832 Remote Similarity NPC202898
0.6832 Remote Similarity NPC475319
0.6813 Remote Similarity NPC470009
0.6804 Remote Similarity NPC20028
0.679 Remote Similarity NPC321873
0.6774 Remote Similarity NPC110072
0.6771 Remote Similarity NPC472273
0.6765 Remote Similarity NPC273002
0.6765 Remote Similarity NPC236753
0.6765 Remote Similarity NPC94086
0.6765 Remote Similarity NPC233433
0.6765 Remote Similarity NPC473817
0.6765 Remote Similarity NPC228190
0.6765 Remote Similarity NPC92297

  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 NPC216883 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
0.8228 Intermediate Similarity NPD7329 Approved
0.7887 Intermediate Similarity NPD6123 Approved
0.725 Intermediate Similarity NPD3181 Approved
0.7051 Intermediate Similarity NPD896 Approved
0.7051 Intermediate Similarity NPD898 Approved
0.7051 Intermediate Similarity NPD897 Approved
0.7042 Intermediate Similarity NPD3730 Approved
0.7042 Intermediate Similarity NPD3728 Approved
0.7042 Intermediate Similarity NPD7346 Approved
0.6901 Remote Similarity NPD892 Phase 3
0.6901 Remote Similarity NPD890 Clinical (unspecified phase)
0.6901 Remote Similarity NPD891 Phase 3
0.6901 Remote Similarity NPD893 Approved
0.6901 Remote Similarity NPD888 Phase 3
0.6761 Remote Similarity NPD2269 Approved
0.67 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8138 Approved
0.6667 Remote Similarity NPD8085 Approved
0.6667 Remote Similarity NPD8082 Approved
0.6667 Remote Similarity NPD8083 Approved
0.6667 Remote Similarity NPD8084 Approved
0.6667 Remote Similarity NPD8086 Approved
0.6667 Remote Similarity NPD8139 Approved
0.6634 Remote Similarity NPD8393 Approved
0.662 Remote Similarity NPD905 Approved
0.662 Remote Similarity NPD904 Phase 3
0.66 Remote Similarity NPD8275 Approved
0.66 Remote Similarity NPD8276 Approved
0.6535 Remote Similarity NPD8081 Approved
0.6509 Remote Similarity NPD8133 Approved
0.65 Remote Similarity NPD7140 Approved
0.65 Remote Similarity NPD7141 Clinical (unspecified phase)
0.65 Remote Similarity NPD7139 Approved
0.6442 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6438 Remote Similarity NPD887 Approved
0.6438 Remote Similarity NPD895 Approved
0.6438 Remote Similarity NPD889 Approved
0.6438 Remote Similarity NPD894 Approved
0.64 Remote Similarity NPD2267 Suspended
0.6329 Remote Similarity NPD8961 Approved
0.6321 Remote Similarity NPD8413 Clinical (unspecified phase)
0.6264 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6264 Remote Similarity NPD3669 Approved
0.625 Remote Similarity NPD8307 Discontinued
0.625 Remote Similarity NPD8140 Approved
0.625 Remote Similarity NPD7909 Approved
0.6197 Remote Similarity NPD6125 Clinical (unspecified phase)
0.619 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6132 Remote Similarity NPD8305 Approved
0.6132 Remote Similarity NPD8306 Approved
0.6132 Remote Similarity NPD6941 Approved
0.6106 Remote Similarity NPD8515 Approved
0.6106 Remote Similarity NPD8516 Approved
0.6106 Remote Similarity NPD8517 Approved
0.6104 Remote Similarity NPD369 Approved
0.6075 Remote Similarity NPD8087 Discontinued
0.6044 Remote Similarity NPD1780 Approved
0.6044 Remote Similarity NPD1779 Approved
0.6038 Remote Similarity NPD6686 Approved
0.6036 Remote Similarity NPD8295 Clinical (unspecified phase)
0.602 Remote Similarity NPD8171 Discontinued
0.6 Remote Similarity NPD8328 Phase 3
0.5965 Remote Similarity NPD8513 Phase 3
0.5943 Remote Similarity NPD6412 Phase 2
0.5915 Remote Similarity NPD9000 Phase 3
0.5915 Remote Similarity NPD8993 Phase 1
0.5915 Remote Similarity NPD8997 Approved
0.5915 Remote Similarity NPD8998 Phase 2
0.5915 Remote Similarity NPD8999 Phase 3
0.5897 Remote Similarity NPD8959 Approved
0.5877 Remote Similarity NPD8345 Approved
0.5877 Remote Similarity NPD8347 Approved
0.5877 Remote Similarity NPD8346 Approved
0.5865 Remote Similarity NPD8301 Approved
0.5865 Remote Similarity NPD8300 Approved
0.5859 Remote Similarity NPD1446 Phase 3
0.5859 Remote Similarity NPD1447 Phase 3
0.5842 Remote Similarity NPD6428 Approved
0.5816 Remote Similarity NPD6698 Approved
0.5816 Remote Similarity NPD46 Approved
0.5775 Remote Similarity NPD2699 Approved
0.5773 Remote Similarity NPD618 Clinical (unspecified phase)
0.5769 Remote Similarity NPD73 Approved
0.5753 Remote Similarity NPD8965 Approved
0.5753 Remote Similarity NPD8966 Approved
0.5752 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5732 Remote Similarity NPD847 Phase 1
0.5728 Remote Similarity NPD2255 Approved
0.5714 Remote Similarity NPD4802 Phase 2
0.5714 Remote Similarity NPD4238 Approved
0.5714 Remote Similarity NPD3729 Clinical (unspecified phase)
0.569 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5664 Remote Similarity NPD6940 Discontinued
0.5641 Remote Similarity NPD8080 Discontinued
0.5631 Remote Similarity NPD881 Approved
0.5618 Remote Similarity NPD1811 Approved
0.5618 Remote Similarity NPD1810 Approved
0.56 Remote Similarity NPD7983 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