Structure

Physi-Chem Properties

Molecular Weight:  297.19
Volume:  320.904
LogP:  0.25
LogD:  0.088
LogS:  -1.501
# Rotatable Bonds:  10
TPSA:  89.79
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.378
Synthetic Accessibility Score:  3.958
Fsp3:  0.562
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.25
MDCK Permeability:  7.956315675983205e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.025
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.117

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.264
Plasma Protein Binding (PPB):  19.16922950744629%
Volume Distribution (VD):  0.308
Pgp-substrate:  57.4328727722168%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.095
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.248
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.562
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.114
CYP3A4-inhibitor:  0.046
CYP3A4-substrate:  0.156

ADMET: Excretion

Clearance (CL):  4.599
Half-life (T1/2):  0.821

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.072
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.091
Skin Sensitization:  0.491
Carcinogencity:  0.038
Eye Corrosion:  0.003
Eye Irritation:  0.042
Respiratory Toxicity:  0.517

Download Data

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

  Natural Product: NPC235311

Natural Product ID:  NPC235311
Common Name*:   (10R,11S)-10,11-Dihydroxy-N-(2-Hydroxy-2-Methylpropyl)Dodeca-2,6,8-Trienamide
IUPAC Name:   (2E,6Z,8E,10R,11S)-10,11-dihydroxy-N-(2-hydroxy-2-methylpropyl)dodeca-2,6,8-trienamide
Synonyms:  
Standard InCHIKey:  XZFVWEROJZOTMT-AHNVWTARSA-N
Standard InCHI:  InChI=1S/C16H27NO4/c1-13(18)14(19)10-8-6-4-5-7-9-11-15(20)17-12-16(2,3)21/h4,6,8-11,13-14,18-19,21H,5,7,12H2,1-3H3,(H,17,20)/b6-4-,10-8+,11-9+/t13-,14+/m0/s1
SMILES:  OC(=NCC(O)(C)C)/C=C/CC/C=CC=C[C@H]([C@@H](O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2335713
PubChem CID:   71717033
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO33007 nepalese zanthoxylum armatum Species n.a. n.a. pericarp n.a. n.a. PMID[23268719]

☑ 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI = 31.0 % PMID[559013]
NPT27 Others Unspecified Activity = 79.0 % PMID[559013]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 31.0 % PMID[559014]

☑ 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 NPC235311 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 NPC253468
0.918 High Similarity NPC471023
0.875 High Similarity NPC129995
0.875 High Similarity NPC315141
0.8475 Intermediate Similarity NPC269800
0.8475 Intermediate Similarity NPC132669
0.8475 Intermediate Similarity NPC246519
0.8475 Intermediate Similarity NPC184014
0.8475 Intermediate Similarity NPC44193
0.8475 Intermediate Similarity NPC14234
0.8387 Intermediate Similarity NPC74617
0.8387 Intermediate Similarity NPC150505
0.8358 Intermediate Similarity NPC471022
0.8261 Intermediate Similarity NPC314678
0.7812 Intermediate Similarity NPC312826
0.7761 Intermediate Similarity NPC477525
0.7667 Intermediate Similarity NPC243539
0.7667 Intermediate Similarity NPC267340
0.7667 Intermediate Similarity NPC145032
0.7667 Intermediate Similarity NPC54542
0.7667 Intermediate Similarity NPC304223
0.75 Intermediate Similarity NPC267692
0.75 Intermediate Similarity NPC307435
0.7463 Intermediate Similarity NPC77891
0.7424 Intermediate Similarity NPC130807
0.7419 Intermediate Similarity NPC119655
0.7419 Intermediate Similarity NPC303672
0.7313 Intermediate Similarity NPC273614
0.7302 Intermediate Similarity NPC163912
0.7302 Intermediate Similarity NPC167759
0.7302 Intermediate Similarity NPC305288
0.7302 Intermediate Similarity NPC56028
0.7258 Intermediate Similarity NPC195986
0.7188 Intermediate Similarity NPC297020
0.7188 Intermediate Similarity NPC471991
0.7188 Intermediate Similarity NPC471992
0.7188 Intermediate Similarity NPC273023
0.7164 Intermediate Similarity NPC6795
0.7162 Intermediate Similarity NPC288086
0.7077 Intermediate Similarity NPC24216
0.7077 Intermediate Similarity NPC104138
0.7077 Intermediate Similarity NPC477049
0.7077 Intermediate Similarity NPC306420
0.7077 Intermediate Similarity NPC261158
0.7059 Intermediate Similarity NPC29468
0.7031 Intermediate Similarity NPC123669
0.697 Remote Similarity NPC245650
0.6923 Remote Similarity NPC242930
0.6849 Remote Similarity NPC103712
0.6849 Remote Similarity NPC291196
0.679 Remote Similarity NPC228638
0.6714 Remote Similarity NPC477106
0.6667 Remote Similarity NPC187315
0.6618 Remote Similarity NPC321030
0.6522 Remote Similarity NPC329003
0.6522 Remote Similarity NPC326524
0.6522 Remote Similarity NPC322186
0.6522 Remote Similarity NPC325550
0.6517 Remote Similarity NPC469739
0.6515 Remote Similarity NPC124382
0.6515 Remote Similarity NPC13011
0.6486 Remote Similarity NPC249713
0.6444 Remote Similarity NPC175614
0.641 Remote Similarity NPC264417
0.641 Remote Similarity NPC217095
0.6406 Remote Similarity NPC328784
0.6406 Remote Similarity NPC291437
0.6395 Remote Similarity NPC316186
0.6349 Remote Similarity NPC91044
0.6338 Remote Similarity NPC324077
0.6333 Remote Similarity NPC233273
0.6333 Remote Similarity NPC205546
0.6333 Remote Similarity NPC50902
0.6308 Remote Similarity NPC59408
0.6308 Remote Similarity NPC71053
0.6308 Remote Similarity NPC93639
0.6264 Remote Similarity NPC45313
0.625 Remote Similarity NPC55068
0.6203 Remote Similarity NPC476924
0.6197 Remote Similarity NPC258788
0.6184 Remote Similarity NPC45060
0.6184 Remote Similarity NPC280065
0.6154 Remote Similarity NPC189764
0.6154 Remote Similarity NPC474460
0.6145 Remote Similarity NPC82799
0.6129 Remote Similarity NPC138935
0.6118 Remote Similarity NPC477199
0.6087 Remote Similarity NPC197294
0.6087 Remote Similarity NPC8098
0.6087 Remote Similarity NPC183449
0.6044 Remote Similarity NPC262312
0.6044 Remote Similarity NPC156782
0.6044 Remote Similarity NPC35269
0.6044 Remote Similarity NPC158445
0.6044 Remote Similarity NPC70323
0.6044 Remote Similarity NPC157353
0.6044 Remote Similarity NPC54961
0.6044 Remote Similarity NPC282088
0.6044 Remote Similarity NPC23454
0.6032 Remote Similarity NPC160628
0.6029 Remote Similarity NPC110732
0.6027 Remote Similarity NPC182758
0.6 Remote Similarity NPC153538
0.6 Remote Similarity NPC182632
0.6 Remote Similarity NPC282705
0.5974 Remote Similarity NPC137620
0.5974 Remote Similarity NPC474675
0.5972 Remote Similarity NPC309877
0.597 Remote Similarity NPC35756
0.5968 Remote Similarity NPC116934
0.5968 Remote Similarity NPC86121
0.5968 Remote Similarity NPC470439
0.5942 Remote Similarity NPC329686
0.5942 Remote Similarity NPC227135
0.5915 Remote Similarity NPC325734
0.5909 Remote Similarity NPC72699
0.5904 Remote Similarity NPC313911
0.5904 Remote Similarity NPC314854
0.5897 Remote Similarity NPC474674
0.5897 Remote Similarity NPC324638
0.5889 Remote Similarity NPC139782
0.5889 Remote Similarity NPC209047
0.5889 Remote Similarity NPC74672
0.5889 Remote Similarity NPC43074
0.5889 Remote Similarity NPC242503
0.587 Remote Similarity NPC3568
0.587 Remote Similarity NPC192066
0.587 Remote Similarity NPC17290
0.587 Remote Similarity NPC256570
0.5857 Remote Similarity NPC4881
0.5824 Remote Similarity NPC15851
0.5824 Remote Similarity NPC309898
0.5824 Remote Similarity NPC263545
0.5824 Remote Similarity NPC475125
0.5824 Remote Similarity NPC186840
0.5824 Remote Similarity NPC473581
0.5824 Remote Similarity NPC473950
0.5824 Remote Similarity NPC111567
0.5824 Remote Similarity NPC473604
0.5821 Remote Similarity NPC151782
0.5821 Remote Similarity NPC473672
0.5821 Remote Similarity NPC200772
0.5821 Remote Similarity NPC474495
0.5806 Remote Similarity NPC206906
0.5784 Remote Similarity NPC29501
0.5781 Remote Similarity NPC140501
0.5775 Remote Similarity NPC472445
0.5769 Remote Similarity NPC127145
0.5769 Remote Similarity NPC475930
0.5758 Remote Similarity NPC267110
0.5758 Remote Similarity NPC248884
0.5758 Remote Similarity NPC31194
0.5758 Remote Similarity NPC85079
0.5758 Remote Similarity NPC302310
0.5738 Remote Similarity NPC56917
0.5714 Remote Similarity NPC55336
0.5714 Remote Similarity NPC281590
0.57 Remote Similarity NPC315426
0.5698 Remote Similarity NPC474312
0.5694 Remote Similarity NPC181872
0.5694 Remote Similarity NPC210999
0.5692 Remote Similarity NPC35141
0.5692 Remote Similarity NPC124183
0.5692 Remote Similarity NPC282097
0.5692 Remote Similarity NPC180575
0.5692 Remote Similarity NPC157096
0.5682 Remote Similarity NPC3210
0.5679 Remote Similarity NPC315843
0.5676 Remote Similarity NPC55376
0.5658 Remote Similarity NPC308844
0.5658 Remote Similarity NPC7940
0.5658 Remote Similarity NPC273600
0.5658 Remote Similarity NPC478098
0.5658 Remote Similarity NPC478099
0.5658 Remote Similarity NPC476586
0.5652 Remote Similarity NPC474496
0.5652 Remote Similarity NPC61177
0.5645 Remote Similarity NPC269823
0.5641 Remote Similarity NPC23721
0.5634 Remote Similarity NPC324224
0.5634 Remote Similarity NPC472808
0.5625 Remote Similarity NPC159547
0.5616 Remote Similarity NPC318306
0.5616 Remote Similarity NPC329249
0.5616 Remote Similarity NPC322002
0.561 Remote Similarity NPC212008
0.561 Remote Similarity NPC62293
0.561 Remote Similarity NPC51055
0.561 Remote Similarity NPC140327
0.56 Remote Similarity NPC476584
0.56 Remote Similarity NPC316674

  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 NPC235311 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
0.625 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6 Remote Similarity NPD205 Approved
0.5915 Remote Similarity NPD585 Clinical (unspecified phase)
0.5897 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5889 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5781 Remote Similarity NPD4265 Approved
0.5781 Remote Similarity NPD860 Phase 2
0.573 Remote Similarity NPD723 Phase 2
0.5714 Remote Similarity NPD6095 Approved
0.5714 Remote Similarity NPD6094 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