Structure

Physi-Chem Properties

Molecular Weight:  1416.79
Volume:  1383.222
LogP:  5.154
LogD:  4.051
LogS:  -3.444
# Rotatable Bonds:  28
TPSA:  446.58
# H-Bond Aceptor:  30
# H-Bond Donor:  14
# Rings:  7
# Heavy Atoms:  30

MedChem Properties

QED Drug-Likeness Score:  0.04
Synthetic Accessibility Score:  7.867
Fsp3:  0.971
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:  -5.782
MDCK Permeability:  8.336555765708908e-05
Pgp-inhibitor:  0.03
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.998
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.952

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  90.2197036743164%
Volume Distribution (VD):  -0.107
Pgp-substrate:  11.626214981079102%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.035
CYP2C19-inhibitor:  0.004
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.006
CYP2D6-inhibitor:  0.026
CYP2D6-substrate:  0.003
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  0.26
Half-life (T1/2):  0.723

ADMET: Toxicity

hERG Blockers:  0.834
Human Hepatotoxicity (H-HT):  0.089
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.085
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.0
Skin Sensitization:  0.946
Carcinogencity:  0.098
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.016

Download Data

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

  Natural Product: NPC475425

Natural Product ID:  NPC475425
Common Name*:   Tricolorin J
IUPAC Name:   n.a.
Synonyms:   Tricolorin J
Standard InCHIKey:  QWUWLJGWZIRUIL-XAQZKAGSSA-N
Standard InCHI:  InChI=1S/C68H120O30/c1-7-9-21-27-39(90-64-59(53(80)47(74)36(4)87-64)97-67-61(55(82)49(76)41(33-69)92-67)95-63-57(84)51(78)45(72)35(3)86-63)29-23-17-13-11-15-19-25-31-43(70)85-34-42-50(77)56(83)62-68(93-42)98-60-54(81)48(75)37(5)88-65(60)91-40(28-22-10-8-2)30-24-18-14-12-16-20-26-32-44(71)94-58-52(79)46(73)38(6)89-66(58)96-62/h35-42,45-69,72-84H,7-34H2,1-6H3/t35-,36-,37-,38-,39-,40+,41-,42-,45-,46-,47+,48+,49-,50-,51+,52+,53+,54+,55+,56+,57-,58-,59-,60-,61-,62-,63+,64+,65+,66+,67+,68+/m1/s1
SMILES:  CCCCCC1CCCCCCCCCC(=O)OC2C(C(C(OC2OC3C(C(C(OC3OC4C(C(C(OC4O1)C)O)O)COC(=O)CCCCCCCCCC(CCCCC)OC5C(C(C(C(O5)C)O)O)OC6C(C(C(C(O6)CO)O)O)OC7C(C(C(C(O7)C)O)O)O)O)O)C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL505421
PubChem CID:   44575283
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
NPO24622 Ipomoea tricolor Species Convolvulaceae Eukaryota crude resin Mexican n.a. DOI[10.1016/S0040-4020(97)00607-8]
NPO24622 Ipomoea tricolor Species Convolvulaceae Eukaryota crude resin Mexican n.a. PMID[16562846]
NPO24622 Ipomoea tricolor Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[8496705]
NPO24622 Ipomoea tricolor Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24622 Ipomoea tricolor Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24622 Ipomoea tricolor Species Convolvulaceae 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 > 256.0 ug.mL-1 PMID[471014]

☑ 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 NPC475425 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 NPC146380
1.0 High Similarity NPC477323
1.0 High Similarity NPC477328
1.0 High Similarity NPC477320
1.0 High Similarity NPC477329
1.0 High Similarity NPC281563
1.0 High Similarity NPC109887
1.0 High Similarity NPC113745
1.0 High Similarity NPC477326
1.0 High Similarity NPC477325
1.0 High Similarity NPC477330
0.973 High Similarity NPC267592
0.9722 High Similarity NPC477350
0.96 High Similarity NPC183888
0.96 High Similarity NPC477331
0.96 High Similarity NPC472205
0.96 High Similarity NPC307400
0.96 High Similarity NPC472204
0.96 High Similarity NPC169345
0.96 High Similarity NPC44782
0.96 High Similarity NPC143421
0.96 High Similarity NPC477317
0.96 High Similarity NPC259294
0.96 High Similarity NPC126685
0.96 High Similarity NPC472201
0.96 High Similarity NPC27289
0.96 High Similarity NPC477319
0.96 High Similarity NPC123204
0.96 High Similarity NPC472203
0.96 High Similarity NPC89843
0.96 High Similarity NPC290012
0.96 High Similarity NPC472202
0.96 High Similarity NPC119583
0.96 High Similarity NPC477318
0.96 High Similarity NPC472200
0.96 High Similarity NPC115013
0.96 High Similarity NPC224953
0.96 High Similarity NPC184915
0.9589 High Similarity NPC476781
0.9589 High Similarity NPC476782
0.9589 High Similarity NPC216883
0.9589 High Similarity NPC476783
0.9351 High Similarity NPC60849
0.9351 High Similarity NPC477332
0.9351 High Similarity NPC472352
0.9333 High Similarity NPC158302
0.9333 High Similarity NPC294748
0.9333 High Similarity NPC146992
0.9333 High Similarity NPC22742
0.9333 High Similarity NPC477344
0.9333 High Similarity NPC477346
0.9333 High Similarity NPC85759
0.9306 High Similarity NPC9763
0.9306 High Similarity NPC206823
0.9306 High Similarity NPC169085
0.9306 High Similarity NPC163812
0.9306 High Similarity NPC225748
0.9306 High Similarity NPC39266
0.9091 High Similarity NPC475327
0.9091 High Similarity NPC269318
0.9091 High Similarity NPC186992
0.9091 High Similarity NPC476087
0.9091 High Similarity NPC475667
0.9091 High Similarity NPC238056
0.9091 High Similarity NPC297768
0.9091 High Similarity NPC173328
0.9091 High Similarity NPC477347
0.9091 High Similarity NPC475270
0.9028 High Similarity NPC52268
0.9028 High Similarity NPC53760
0.8889 High Similarity NPC211428
0.8889 High Similarity NPC285003
0.8889 High Similarity NPC241265
0.875 High Similarity NPC67099
0.875 High Similarity NPC97736
0.875 High Similarity NPC250619
0.875 High Similarity NPC50228
0.8611 High Similarity NPC206601
0.8333 Intermediate Similarity NPC190418
0.8333 Intermediate Similarity NPC76881
0.8333 Intermediate Similarity NPC471760
0.8333 Intermediate Similarity NPC12040
0.8333 Intermediate Similarity NPC471761
0.8289 Intermediate Similarity NPC308096
0.8289 Intermediate Similarity NPC291228
0.8276 Intermediate Similarity NPC163409
0.8276 Intermediate Similarity NPC44682
0.8194 Intermediate Similarity NPC6848
0.8158 Intermediate Similarity NPC185419
0.8158 Intermediate Similarity NPC184550
0.8056 Intermediate Similarity NPC325773
0.8046 Intermediate Similarity NPC477349
0.7865 Intermediate Similarity NPC477348
0.7865 Intermediate Similarity NPC477345
0.7865 Intermediate Similarity NPC238264
0.7831 Intermediate Similarity NPC248415
0.7778 Intermediate Similarity NPC477750
0.7778 Intermediate Similarity NPC477753
0.7778 Intermediate Similarity NPC477757
0.7778 Intermediate Similarity NPC477763
0.7778 Intermediate Similarity NPC477762
0.7778 Intermediate Similarity NPC477755
0.7738 Intermediate Similarity NPC156089
0.7738 Intermediate Similarity NPC470313
0.7738 Intermediate Similarity NPC473500
0.7738 Intermediate Similarity NPC38295
0.7692 Intermediate Similarity NPC475241
0.7692 Intermediate Similarity NPC473765
0.7692 Intermediate Similarity NPC473605
0.7692 Intermediate Similarity NPC476066
0.7692 Intermediate Similarity NPC475164
0.7692 Intermediate Similarity NPC475540
0.7692 Intermediate Similarity NPC475593
0.7692 Intermediate Similarity NPC475375
0.7692 Intermediate Similarity NPC475525
0.75 Intermediate Similarity NPC21693
0.75 Intermediate Similarity NPC236649
0.75 Intermediate Similarity NPC317023
0.7386 Intermediate Similarity NPC51662
0.7361 Intermediate Similarity NPC472025
0.7273 Intermediate Similarity NPC477756
0.7273 Intermediate Similarity NPC477751
0.7273 Intermediate Similarity NPC477764
0.7273 Intermediate Similarity NPC477752
0.7222 Intermediate Similarity NPC148424
0.72 Intermediate Similarity NPC22709
0.7179 Intermediate Similarity NPC477754
0.7179 Intermediate Similarity NPC477761
0.7179 Intermediate Similarity NPC477759
0.7179 Intermediate Similarity NPC477760
0.7179 Intermediate Similarity NPC477758
0.7172 Intermediate Similarity NPC126753
0.7159 Intermediate Similarity NPC83839
0.7143 Intermediate Similarity NPC469827
0.7143 Intermediate Similarity NPC231271
0.7143 Intermediate Similarity NPC470519
0.7129 Intermediate Similarity NPC471431
0.71 Intermediate Similarity NPC207693
0.7079 Intermediate Similarity NPC470657
0.7045 Intermediate Similarity NPC288471
0.7027 Intermediate Similarity NPC290179
0.7027 Intermediate Similarity NPC34877
0.7027 Intermediate Similarity NPC322855
0.7027 Intermediate Similarity NPC320032
0.7024 Intermediate Similarity NPC110813
0.7 Intermediate Similarity NPC471430
0.7 Intermediate Similarity NPC31349
0.7 Intermediate Similarity NPC314364
0.7 Intermediate Similarity NPC287269
0.6962 Remote Similarity NPC32148
0.6961 Remote Similarity NPC470622
0.6944 Remote Similarity NPC303727
0.6944 Remote Similarity NPC23155
0.6944 Remote Similarity NPC469937
0.6944 Remote Similarity NPC320588
0.6944 Remote Similarity NPC53463
0.6941 Remote Similarity NPC133377
0.6939 Remote Similarity NPC310031
0.6939 Remote Similarity NPC80191
0.6931 Remote Similarity NPC231566
0.6931 Remote Similarity NPC473688
0.6931 Remote Similarity NPC262567
0.6931 Remote Similarity NPC471626
0.6931 Remote Similarity NPC469826
0.6907 Remote Similarity NPC471426
0.6907 Remote Similarity NPC471427
0.6907 Remote Similarity NPC471428
0.69 Remote Similarity NPC273189
0.69 Remote Similarity NPC184805
0.6883 Remote Similarity NPC268243
0.6863 Remote Similarity NPC233433
0.6863 Remote Similarity NPC220836
0.6863 Remote Similarity NPC473817
0.6863 Remote Similarity NPC228190
0.6863 Remote Similarity NPC92297
0.6863 Remote Similarity NPC94086
0.6863 Remote Similarity NPC273002
0.6863 Remote Similarity NPC236753
0.6863 Remote Similarity NPC469825
0.6857 Remote Similarity NPC293330
0.6857 Remote Similarity NPC250247
0.6857 Remote Similarity NPC469782
0.6857 Remote Similarity NPC60557
0.6857 Remote Similarity NPC41061
0.6857 Remote Similarity NPC67857
0.6857 Remote Similarity NPC227551
0.6857 Remote Similarity NPC65105
0.6857 Remote Similarity NPC305981
0.6857 Remote Similarity NPC294453
0.6857 Remote Similarity NPC473714
0.6857 Remote Similarity NPC119592
0.6857 Remote Similarity NPC475160
0.6857 Remote Similarity NPC100639
0.6857 Remote Similarity NPC236638
0.6857 Remote Similarity NPC79643
0.6857 Remote Similarity NPC161717
0.6857 Remote Similarity NPC76972
0.6857 Remote Similarity NPC309907
0.6857 Remote Similarity NPC202828
0.6857 Remote Similarity NPC123199

  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 NPC475425 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
0.8125 Intermediate Similarity NPD7329 Approved
0.7778 Intermediate Similarity NPD6123 Approved
0.716 Intermediate Similarity NPD3181 Approved
0.6962 Remote Similarity NPD896 Approved
0.6962 Remote Similarity NPD897 Approved
0.6962 Remote Similarity NPD898 Approved
0.6944 Remote Similarity NPD7346 Approved
0.6944 Remote Similarity NPD3730 Approved
0.6944 Remote Similarity NPD3728 Approved
0.6806 Remote Similarity NPD891 Phase 3
0.6806 Remote Similarity NPD888 Phase 3
0.6806 Remote Similarity NPD893 Approved
0.6806 Remote Similarity NPD892 Phase 3
0.6806 Remote Similarity NPD890 Clinical (unspecified phase)
0.6667 Remote Similarity NPD2269 Approved
0.6634 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6604 Remote Similarity NPD8133 Approved
0.6571 Remote Similarity NPD8413 Clinical (unspecified phase)
0.6528 Remote Similarity NPD905 Approved
0.6528 Remote Similarity NPD904 Phase 3
0.6436 Remote Similarity NPD8083 Approved
0.6436 Remote Similarity NPD8138 Approved
0.6436 Remote Similarity NPD7141 Clinical (unspecified phase)
0.6436 Remote Similarity NPD8085 Approved
0.6436 Remote Similarity NPD7140 Approved
0.6436 Remote Similarity NPD8139 Approved
0.6436 Remote Similarity NPD7139 Approved
0.6436 Remote Similarity NPD8086 Approved
0.6436 Remote Similarity NPD8084 Approved
0.6436 Remote Similarity NPD8082 Approved
0.6408 Remote Similarity NPD8393 Approved
0.6381 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6373 Remote Similarity NPD8276 Approved
0.6373 Remote Similarity NPD8275 Approved
0.6351 Remote Similarity NPD889 Approved
0.6351 Remote Similarity NPD894 Approved
0.6351 Remote Similarity NPD895 Approved
0.6351 Remote Similarity NPD887 Approved
0.6316 Remote Similarity NPD2267 Suspended
0.6311 Remote Similarity NPD8081 Approved
0.625 Remote Similarity NPD8961 Approved
0.6196 Remote Similarity NPD3669 Approved
0.6196 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6195 Remote Similarity NPD8515 Approved
0.6195 Remote Similarity NPD8516 Approved
0.6195 Remote Similarity NPD8517 Approved
0.619 Remote Similarity NPD8307 Discontinued
0.619 Remote Similarity NPD8140 Approved
0.6173 Remote Similarity NPD7909 Approved
0.6126 Remote Similarity NPD8295 Clinical (unspecified phase)
0.6122 Remote Similarity NPD8171 Discontinued
0.6118 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6111 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6075 Remote Similarity NPD8306 Approved
0.6075 Remote Similarity NPD6941 Approved
0.6075 Remote Similarity NPD8305 Approved
0.6053 Remote Similarity NPD8513 Phase 3
0.6026 Remote Similarity NPD369 Approved
0.6019 Remote Similarity NPD8087 Discontinued
0.5981 Remote Similarity NPD6686 Approved
0.5978 Remote Similarity NPD1780 Approved
0.5978 Remote Similarity NPD1779 Approved
0.5948 Remote Similarity NPD8328 Phase 3
0.5833 Remote Similarity NPD8997 Approved
0.5833 Remote Similarity NPD9000 Phase 3
0.5833 Remote Similarity NPD8998 Phase 2
0.5833 Remote Similarity NPD8999 Phase 3
0.5833 Remote Similarity NPD8993 Phase 1
0.5826 Remote Similarity NPD8346 Approved
0.5826 Remote Similarity NPD8345 Approved
0.5826 Remote Similarity NPD8347 Approved
0.5823 Remote Similarity NPD8959 Approved
0.58 Remote Similarity NPD1447 Phase 3
0.58 Remote Similarity NPD1446 Phase 3
0.5784 Remote Similarity NPD6428 Approved
0.5758 Remote Similarity NPD6698 Approved
0.5758 Remote Similarity NPD46 Approved
0.5741 Remote Similarity NPD6412 Phase 2
0.5714 Remote Similarity NPD618 Clinical (unspecified phase)
0.5702 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5696 Remote Similarity NPD73 Approved
0.5694 Remote Similarity NPD2699 Approved
0.5676 Remote Similarity NPD8966 Approved
0.5676 Remote Similarity NPD8965 Approved
0.5673 Remote Similarity NPD2255 Approved
0.5663 Remote Similarity NPD847 Phase 1
0.566 Remote Similarity NPD8300 Approved
0.566 Remote Similarity NPD8301 Approved
0.5641 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5614 Remote Similarity NPD6940 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