Structure

Physi-Chem Properties

Molecular Weight:  294.27
Volume:  336.839
LogP:  2.195
LogD:  3.064
LogS:  -1.99
# Rotatable Bonds:  10
TPSA:  58.28
# H-Bond Aceptor:  3
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.428
Synthetic Accessibility Score:  4.025
Fsp3:  0.778
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:  -5.072
MDCK Permeability:  7.985064257809427e-06
Pgp-inhibitor:  0.055
Pgp-substrate:  0.953
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  0.726
30% Bioavailability (F30%):  0.825

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.064
Plasma Protein Binding (PPB):  56.20970153808594%
Volume Distribution (VD):  0.748
Pgp-substrate:  35.452049255371094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.102
CYP1A2-substrate:  0.292
CYP2C19-inhibitor:  0.145
CYP2C19-substrate:  0.788
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.356
CYP2D6-inhibitor:  0.806
CYP2D6-substrate:  0.931
CYP3A4-inhibitor:  0.202
CYP3A4-substrate:  0.188

ADMET: Excretion

Clearance (CL):  5.064
Half-life (T1/2):  0.244

ADMET: Toxicity

hERG Blockers:  0.978
Human Hepatotoxicity (H-HT):  0.863
Drug-inuced Liver Injury (DILI):  0.387
AMES Toxicity:  0.038
Rat Oral Acute Toxicity:  0.538
Maximum Recommended Daily Dose:  0.897
Skin Sensitization:  0.952
Carcinogencity:  0.084
Eye Corrosion:  0.93
Eye Irritation:  0.05
Respiratory Toxicity:  0.896

Download Data

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

  Natural Product: NPC473972

Natural Product ID:  NPC473972
Common Name*:   Pseudodistomin E
IUPAC Name:   (2R,4S,5R)-5-amino-2-[(6E,8E)-trideca-6,8-dienyl]piperidin-4-ol
Synonyms:   Pseudodistomin E
Standard InCHIKey:  ACYWLYLTIGBFNS-YHOZXLMLSA-N
Standard InCHI:  InChI=1S/C18H34N2O/c1-2-3-4-5-6-7-8-9-10-11-12-13-16-14-18(21)17(19)15-20-16/h5-8,16-18,20-21H,2-4,9-15,19H2,1H3/b6-5+,8-7+/t16-,17-,18+/m1/s1
SMILES:  CCCC/C=C/C=C/CCCCC[C@H]1NC[C@H]([C@H](C1)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL456861
PubChem CID:   10424557
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives

*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
NPO28004 Pseudodistoma megalarva Species Pseudodistomidae Eukaryota n.a. n.a. n.a. PMID[9358640]
NPO28004 Pseudodistoma megalarva Species Pseudodistomidae 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
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 4.3 ug PMID[485981]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 12.0 ug PMID[485981]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 1.8 ug PMID[485981]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae Activity = 2.3 ug PMID[485981]

☑ 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 NPC473972 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 NPC473971
1.0 High Similarity NPC475363
0.9178 High Similarity NPC78562
0.9178 High Similarity NPC473588
0.8533 High Similarity NPC26932
0.7973 Intermediate Similarity NPC113224
0.7763 Intermediate Similarity NPC23721
0.7432 Intermediate Similarity NPC47333
0.7361 Intermediate Similarity NPC302569
0.7361 Intermediate Similarity NPC168308
0.7284 Intermediate Similarity NPC470993
0.7284 Intermediate Similarity NPC470992
0.7195 Intermediate Similarity NPC3094
0.7021 Intermediate Similarity NPC119225
0.7021 Intermediate Similarity NPC471635
0.7021 Intermediate Similarity NPC470382
0.7021 Intermediate Similarity NPC25033
0.7021 Intermediate Similarity NPC476261
0.6988 Remote Similarity NPC51055
0.6988 Remote Similarity NPC140327
0.6988 Remote Similarity NPC212008
0.6988 Remote Similarity NPC62293
0.6977 Remote Similarity NPC209232
0.6883 Remote Similarity NPC55068
0.6786 Remote Similarity NPC34672
0.6782 Remote Similarity NPC79367
0.6707 Remote Similarity NPC476694
0.6707 Remote Similarity NPC476695
0.6707 Remote Similarity NPC476696
0.6591 Remote Similarity NPC207657
0.6588 Remote Similarity NPC217095
0.6588 Remote Similarity NPC264417
0.6531 Remote Similarity NPC474164
0.6506 Remote Similarity NPC306973
0.65 Remote Similarity NPC118275
0.6471 Remote Similarity NPC477000
0.6471 Remote Similarity NPC470994
0.6471 Remote Similarity NPC477001
0.6463 Remote Similarity NPC268922
0.6438 Remote Similarity NPC474322
0.64 Remote Similarity NPC135799
0.6386 Remote Similarity NPC291196
0.6386 Remote Similarity NPC103712
0.6364 Remote Similarity NPC473695
0.6364 Remote Similarity NPC473446
0.6341 Remote Similarity NPC471418
0.631 Remote Similarity NPC324638
0.6286 Remote Similarity NPC159367
0.6282 Remote Similarity NPC329003
0.6282 Remote Similarity NPC326524
0.6282 Remote Similarity NPC325550
0.6275 Remote Similarity NPC176012
0.625 Remote Similarity NPC477106
0.6222 Remote Similarity NPC476560
0.6216 Remote Similarity NPC123814
0.6214 Remote Similarity NPC55336
0.6207 Remote Similarity NPC477002
0.6154 Remote Similarity NPC321030
0.6111 Remote Similarity NPC96966
0.6111 Remote Similarity NPC121062
0.6111 Remote Similarity NPC29222
0.6104 Remote Similarity NPC8979
0.6098 Remote Similarity NPC303798
0.6098 Remote Similarity NPC286851
0.6092 Remote Similarity NPC288086
0.6058 Remote Similarity NPC473254
0.6038 Remote Similarity NPC315426
0.6026 Remote Similarity NPC204709
0.6 Remote Similarity NPC474833
0.6 Remote Similarity NPC311164
0.6 Remote Similarity NPC272732
0.5982 Remote Similarity NPC101139
0.598 Remote Similarity NPC315170
0.5978 Remote Similarity NPC82799
0.5976 Remote Similarity NPC75435
0.5976 Remote Similarity NPC198341
0.5976 Remote Similarity NPC471892
0.5976 Remote Similarity NPC471780
0.5976 Remote Similarity NPC142290
0.5976 Remote Similarity NPC223386
0.5957 Remote Similarity NPC477199
0.5949 Remote Similarity NPC193593
0.5949 Remote Similarity NPC216415
0.5949 Remote Similarity NPC476537
0.5949 Remote Similarity NPC290106
0.5949 Remote Similarity NPC143809
0.5949 Remote Similarity NPC76726
0.593 Remote Similarity NPC97614
0.5921 Remote Similarity NPC277072
0.5921 Remote Similarity NPC178263
0.5905 Remote Similarity NPC476877
0.5893 Remote Similarity NPC28280
0.5893 Remote Similarity NPC304646
0.5882 Remote Similarity NPC474812
0.5862 Remote Similarity NPC474468
0.5859 Remote Similarity NPC475603
0.5859 Remote Similarity NPC61894
0.5849 Remote Similarity NPC150254
0.5849 Remote Similarity NPC147000
0.5849 Remote Similarity NPC304761
0.5849 Remote Similarity NPC226778
0.5833 Remote Similarity NPC76976
0.5814 Remote Similarity NPC473710
0.5814 Remote Similarity NPC475694
0.5795 Remote Similarity NPC305223
0.5794 Remote Similarity NPC477292
0.5794 Remote Similarity NPC476876
0.5789 Remote Similarity NPC49494
0.5789 Remote Similarity NPC188341
0.5789 Remote Similarity NPC475975
0.5783 Remote Similarity NPC206660
0.578 Remote Similarity NPC85001
0.578 Remote Similarity NPC95920
0.578 Remote Similarity NPC147835
0.578 Remote Similarity NPC253645
0.5769 Remote Similarity NPC242930
0.5766 Remote Similarity NPC314306
0.5761 Remote Similarity NPC314762
0.5758 Remote Similarity NPC84171
0.5758 Remote Similarity NPC319021
0.575 Remote Similarity NPC471421
0.575 Remote Similarity NPC233364
0.5745 Remote Similarity NPC474312
0.5732 Remote Similarity NPC69669
0.5732 Remote Similarity NPC150680
0.5732 Remote Similarity NPC218150
0.5732 Remote Similarity NPC306462
0.5732 Remote Similarity NPC17455
0.5732 Remote Similarity NPC22774
0.5732 Remote Similarity NPC2432
0.5728 Remote Similarity NPC91036
0.5714 Remote Similarity NPC477525
0.5714 Remote Similarity NPC316186
0.5696 Remote Similarity NPC471605
0.5696 Remote Similarity NPC471443
0.5679 Remote Similarity NPC319131
0.5673 Remote Similarity NPC132931
0.5673 Remote Similarity NPC91604
0.5663 Remote Similarity NPC471419
0.5663 Remote Similarity NPC163134
0.566 Remote Similarity NPC325339
0.566 Remote Similarity NPC327226
0.566 Remote Similarity NPC473289
0.566 Remote Similarity NPC72401
0.566 Remote Similarity NPC471258
0.5658 Remote Similarity NPC261571
0.5631 Remote Similarity NPC476903
0.5618 Remote Similarity NPC314678
0.5618 Remote Similarity NPC208657
0.5607 Remote Similarity NPC241879

  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 NPC473972 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
0.6883 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6389 Remote Similarity NPD3214 Discontinued
0.631 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6216 Remote Similarity NPD3215 Phase 1
0.5982 Remote Similarity NPD7508 Discontinued
0.5849 Remote Similarity NPD314 Approved
0.5849 Remote Similarity NPD315 Approved
0.5849 Remote Similarity NPD309 Approved
0.5849 Remote Similarity NPD10 Approved
0.5849 Remote Similarity NPD310 Approved
0.5849 Remote Similarity NPD311 Approved
0.5766 Remote Similarity NPD6429 Approved
0.5766 Remote Similarity NPD6430 Approved
0.5732 Remote Similarity NPD9028 Phase 2
0.5732 Remote Similarity NPD9026 Phase 2
0.5732 Remote Similarity NPD9029 Phase 3
0.5732 Remote Similarity NPD9027 Phase 3
0.5732 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5682 Remote Similarity NPD5365 Phase 2
0.5652 Remote Similarity NPD3732 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