Structure

Physi-Chem Properties

Molecular Weight:  471.28
Volume:  497.933
LogP:  4.692
LogD:  4.029
LogS:  -5.099
# Rotatable Bonds:  20
TPSA:  65.07
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.063
Synthetic Accessibility Score:  3.965
Fsp3:  0.68
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.578
MDCK Permeability:  3.211459261365235e-05
Pgp-inhibitor:  0.408
Pgp-substrate:  0.014
Human Intestinal Absorption (HIA):  0.134
20% Bioavailability (F20%):  0.14
30% Bioavailability (F30%):  0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.998
Plasma Protein Binding (PPB):  87.62681579589844%
Volume Distribution (VD):  0.48
Pgp-substrate:  5.848413944244385%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.38
CYP2C19-inhibitor:  0.464
CYP2C19-substrate:  0.909
CYP2C9-inhibitor:  0.56
CYP2C9-substrate:  0.253
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.615
CYP3A4-inhibitor:  0.939
CYP3A4-substrate:  0.281

ADMET: Excretion

Clearance (CL):  4.995
Half-life (T1/2):  0.879

ADMET: Toxicity

hERG Blockers:  0.176
Human Hepatotoxicity (H-HT):  0.776
Drug-inuced Liver Injury (DILI):  0.405
AMES Toxicity:  0.433
Rat Oral Acute Toxicity:  0.031
Maximum Recommended Daily Dose:  0.841
Skin Sensitization:  0.986
Carcinogencity:  0.591
Eye Corrosion:  0.94
Eye Irritation:  0.435
Respiratory Toxicity:  0.923

Download Data

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

  Natural Product: NPC81195

Natural Product ID:  NPC81195
Common Name*:   Malyngamide O
IUPAC Name:   methyl (2E,5Z)-6-chloro-3-methoxy-5-[[[(E,7S)-7-methoxytetradec-4-enoyl]-methylamino]methyl]hexa-2,5-dienoate
Synonyms:   Malyngamide O
Standard InCHIKey:  APYMXRPHYRRJTM-ZWUHNMOSSA-N
Standard InCHI:  InChI=1S/C25H42ClNO5/c1-6-7-8-9-11-14-22(30-3)15-12-10-13-16-24(28)27(2)20-21(19-26)17-23(31-4)18-25(29)32-5/h10,12,18-19,22H,6-9,11,13-17,20H2,1-5H3/b12-10+,21-19-,23-18+/t22-/m0/s1
SMILES:  CCCCCCC[C@@H](C/C=C/CCC(=O)N(C/C(=CCl)/C/C(=CC(=O)OC)/OC)C)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL485986
PubChem CID:   10027764
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters

*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
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. DOI[10.1021/np960188t]
NPO4302 Stylocheilus longicauda Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[10924193]
NPO4302 Stylocheilus longicauda Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[11076568]
NPO16759 Polyalthia debilis Species Annonaceae Eukaryota n.a. root n.a. PMID[12762793]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. PMID[16595909]
NPO12302 Hebanthe paniculata Species Amaranthaceae Eukaryota n.a. root n.a. PMID[19941264]
NPO16759 Polyalthia debilis Species Annonaceae Eukaryota Roots n.a. n.a. PMID[20795741]
NPO4302 Stylocheilus longicauda Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[4833645]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12302 Hebanthe paniculata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16176 Citrus fusca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16759 Polyalthia debilis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15140 Soja max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21487 Eunicea flexuosa Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13233 Solanum megacarpum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12302 Hebanthe paniculata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12135 Rhamnus triquetra Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3396 Allium cernuum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4302 Stylocheilus longicauda Species Aplysiidae 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
NPT168 Cell Line P388 Mus musculus IC50 = 2.0 ug.mL-1 PMID[566448]
NPT81 Cell Line A549 Homo sapiens IC50 = 2.0 ug.mL-1 PMID[566448]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 2.0 ug.mL-1 PMID[566448]

☑ 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 NPC81195 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
0.8352 Intermediate Similarity NPC53240
0.75 Intermediate Similarity NPC233932
0.7264 Intermediate Similarity NPC21324
0.7129 Intermediate Similarity NPC52820
0.6952 Remote Similarity NPC474828
0.6952 Remote Similarity NPC474827
0.6952 Remote Similarity NPC199831
0.6952 Remote Similarity NPC68001
0.6882 Remote Similarity NPC477523
0.6857 Remote Similarity NPC474244
0.6809 Remote Similarity NPC477524
0.6774 Remote Similarity NPC471768
0.6697 Remote Similarity NPC474099
0.6535 Remote Similarity NPC159568
0.6476 Remote Similarity NPC476344
0.6465 Remote Similarity NPC130436
0.6465 Remote Similarity NPC469860
0.6465 Remote Similarity NPC469861
0.6458 Remote Similarity NPC226982
0.6458 Remote Similarity NPC277341
0.6442 Remote Similarity NPC150041
0.6422 Remote Similarity NPC469604
0.6372 Remote Similarity NPC58281
0.6364 Remote Similarity NPC296589
0.6355 Remote Similarity NPC474985
0.6354 Remote Similarity NPC209232
0.6321 Remote Similarity NPC241426
0.6304 Remote Similarity NPC474705
0.6283 Remote Similarity NPC469603
0.6264 Remote Similarity NPC469660
0.6226 Remote Similarity NPC175614
0.6222 Remote Similarity NPC218477
0.6214 Remote Similarity NPC17143
0.6214 Remote Similarity NPC47230
0.6211 Remote Similarity NPC46268
0.6204 Remote Similarity NPC26597
0.6196 Remote Similarity NPC84038
0.618 Remote Similarity NPC248125
0.617 Remote Similarity NPC34672
0.6168 Remote Similarity NPC150967
0.6168 Remote Similarity NPC265662
0.6147 Remote Similarity NPC77703
0.6126 Remote Similarity NPC205176
0.6106 Remote Similarity NPC470072
0.6082 Remote Similarity NPC473947
0.6068 Remote Similarity NPC474984
0.6055 Remote Similarity NPC316730
0.6042 Remote Similarity NPC325936
0.6 Remote Similarity NPC469414
0.6 Remote Similarity NPC329826
0.6 Remote Similarity NPC188785
0.6 Remote Similarity NPC284447
0.5978 Remote Similarity NPC475004
0.5977 Remote Similarity NPC45097
0.5955 Remote Similarity NPC477456
0.5955 Remote Similarity NPC477457
0.5948 Remote Similarity NPC475608
0.5948 Remote Similarity NPC21713
0.5941 Remote Similarity NPC475975
0.5934 Remote Similarity NPC472266
0.5934 Remote Similarity NPC203335
0.5932 Remote Similarity NPC472536
0.5932 Remote Similarity NPC103391
0.5914 Remote Similarity NPC97614
0.59 Remote Similarity NPC123908
0.59 Remote Similarity NPC10080
0.59 Remote Similarity NPC473810
0.5897 Remote Similarity NPC474995
0.5895 Remote Similarity NPC140287
0.5895 Remote Similarity NPC476355
0.5895 Remote Similarity NPC470994
0.5889 Remote Similarity NPC182794
0.5876 Remote Similarity NPC471225
0.587 Remote Similarity NPC96272
0.587 Remote Similarity NPC474823
0.587 Remote Similarity NPC475760
0.5862 Remote Similarity NPC159650
0.5862 Remote Similarity NPC474267
0.5862 Remote Similarity NPC22897
0.5859 Remote Similarity NPC120335
0.5851 Remote Similarity NPC186531
0.5843 Remote Similarity NPC179087
0.5843 Remote Similarity NPC210303
0.5843 Remote Similarity NPC44343
0.5841 Remote Similarity NPC470073
0.5841 Remote Similarity NPC133420
0.5841 Remote Similarity NPC75523
0.5833 Remote Similarity NPC260396
0.5833 Remote Similarity NPC477421
0.5806 Remote Similarity NPC101622
0.58 Remote Similarity NPC471325
0.58 Remote Similarity NPC112868
0.5795 Remote Similarity NPC79756
0.5789 Remote Similarity NPC329890
0.5789 Remote Similarity NPC252503
0.5789 Remote Similarity NPC185186
0.5789 Remote Similarity NPC329914
0.5789 Remote Similarity NPC327383
0.5789 Remote Similarity NPC154601
0.5789 Remote Similarity NPC271269
0.5778 Remote Similarity NPC206660
0.5773 Remote Similarity NPC123360
0.5769 Remote Similarity NPC478144
0.5761 Remote Similarity NPC194871
0.576 Remote Similarity NPC321197
0.5758 Remote Similarity NPC477088
0.5752 Remote Similarity NPC318544
0.5747 Remote Similarity NPC23418
0.5745 Remote Similarity NPC64234
0.5745 Remote Similarity NPC323677
0.5745 Remote Similarity NPC477429
0.5745 Remote Similarity NPC4299
0.5745 Remote Similarity NPC37929
0.5743 Remote Similarity NPC35556
0.5739 Remote Similarity NPC251330
0.5736 Remote Similarity NPC213969
0.5736 Remote Similarity NPC165726
0.5736 Remote Similarity NPC17374
0.573 Remote Similarity NPC270412
0.573 Remote Similarity NPC252684
0.573 Remote Similarity NPC14437
0.573 Remote Similarity NPC151648
0.5729 Remote Similarity NPC474758
0.5729 Remote Similarity NPC477204
0.5729 Remote Similarity NPC227396
0.5728 Remote Similarity NPC2640
0.5728 Remote Similarity NPC319913
0.5728 Remote Similarity NPC475614
0.5726 Remote Similarity NPC63511
0.5714 Remote Similarity NPC469597
0.5714 Remote Similarity NPC329401
0.5714 Remote Similarity NPC315394
0.5714 Remote Similarity NPC477987
0.5714 Remote Similarity NPC475711
0.5714 Remote Similarity NPC97516
0.5702 Remote Similarity NPC475642
0.5702 Remote Similarity NPC477000
0.5702 Remote Similarity NPC477001
0.5702 Remote Similarity NPC477553
0.5701 Remote Similarity NPC472264
0.5699 Remote Similarity NPC470256
0.5699 Remote Similarity NPC276290
0.5691 Remote Similarity NPC477140
0.5691 Remote Similarity NPC477143
0.5686 Remote Similarity NPC178758
0.5686 Remote Similarity NPC253801
0.5686 Remote Similarity NPC196102
0.5684 Remote Similarity NPC163003
0.5684 Remote Similarity NPC475762
0.5684 Remote Similarity NPC477084
0.5682 Remote Similarity NPC286189
0.5678 Remote Similarity NPC474411
0.5678 Remote Similarity NPC474431
0.5676 Remote Similarity NPC270813
0.5673 Remote Similarity NPC69082
0.5673 Remote Similarity NPC279267
0.5673 Remote Similarity NPC186332
0.5673 Remote Similarity NPC47220
0.5673 Remote Similarity NPC322672
0.567 Remote Similarity NPC285840
0.567 Remote Similarity NPC327041
0.567 Remote Similarity NPC244166
0.5667 Remote Similarity NPC217940
0.5664 Remote Similarity NPC473289
0.5657 Remote Similarity NPC473471
0.5657 Remote Similarity NPC93763
0.5657 Remote Similarity NPC128276
0.5657 Remote Similarity NPC108816
0.5657 Remote Similarity NPC182292
0.5656 Remote Similarity NPC477555
0.5652 Remote Similarity NPC93179
0.5648 Remote Similarity NPC304897
0.5647 Remote Similarity NPC478120
0.5641 Remote Similarity NPC470536
0.5638 Remote Similarity NPC232812
0.5638 Remote Similarity NPC477688
0.5638 Remote Similarity NPC265574
0.5638 Remote Similarity NPC236208
0.5638 Remote Similarity NPC151481
0.5635 Remote Similarity NPC469999
0.5631 Remote Similarity NPC41856
0.5625 Remote Similarity NPC477964
0.5625 Remote Similarity NPC222244
0.5625 Remote Similarity NPC144419
0.5625 Remote Similarity NPC477085
0.5625 Remote Similarity NPC16349
0.5625 Remote Similarity NPC326126
0.5619 Remote Similarity NPC478145
0.5619 Remote Similarity NPC473525
0.5618 Remote Similarity NPC26223
0.5618 Remote Similarity NPC158368
0.5618 Remote Similarity NPC143857
0.5618 Remote Similarity NPC299730
0.5618 Remote Similarity NPC154908
0.5618 Remote Similarity NPC226872
0.5618 Remote Similarity NPC252851
0.5618 Remote Similarity NPC229252
0.5614 Remote Similarity NPC6271
0.5612 Remote Similarity NPC469880
0.5612 Remote Similarity NPC477202

  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 NPC81195 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
0.6522 Remote Similarity NPD1452 Discontinued
0.6279 Remote Similarity NPD3205 Discontinued
0.573 Remote Similarity NPD9418 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1376 Discontinued
0.5691 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5636 Remote Similarity NPD5349 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