Structure

Physi-Chem Properties

Molecular Weight:  208.16
Volume:  224.506
LogP:  -1.184
LogD:  0.631
LogS:  -0.741
# Rotatable Bonds:  2
TPSA:  32.34
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.71
Synthetic Accessibility Score:  3.469
Fsp3:  0.75
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:  -4.777
MDCK Permeability:  1.6878952010301873e-05
Pgp-inhibitor:  0.218
Pgp-substrate:  0.608
Human Intestinal Absorption (HIA):  0.102
20% Bioavailability (F20%):  0.858
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.329
Plasma Protein Binding (PPB):  13.841742515563965%
Volume Distribution (VD):  1.174
Pgp-substrate:  83.95948791503906%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.12
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.371
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.119
CYP2D6-inhibitor:  0.27
CYP2D6-substrate:  0.667
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.289

ADMET: Excretion

Clearance (CL):  4.958
Half-life (T1/2):  0.862

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.538
Drug-inuced Liver Injury (DILI):  0.093
AMES Toxicity:  0.027
Rat Oral Acute Toxicity:  0.559
Maximum Recommended Daily Dose:  0.891
Skin Sensitization:  0.908
Carcinogencity:  0.302
Eye Corrosion:  0.052
Eye Irritation:  0.19
Respiratory Toxicity:  0.912

Download Data

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

  Natural Product: NPC76869

Natural Product ID:  NPC76869
Common Name*:   D-Ammodendrine
IUPAC Name:   1-[5-[(2R)-piperidin-2-yl]-3,4-dihydro-2H-pyridin-1-yl]ethanone
Synonyms:   D-Ammodendrine
Standard InCHIKey:  APKLQIQRPUDADG-GFCCVEGCSA-N
Standard InCHI:  InChI=1S/C12H20N2O/c1-10(15)14-8-4-5-11(9-14)12-6-2-3-7-13-12/h9,12-13H,2-8H2,1H3/p+1/t12-/m1/s1
SMILES:  CC(=O)N1CCCC(=C1)[C@H]1CCCC[NH2+]1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464777
PubChem CID:   442625
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0002224] Hydropyridines
          • [CHEMONTID:0001934] Tetrahydropyridines

*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
NPO6806 Tyromyces fissilis Species Coriolaceae Eukaryota fruit bodies n.a. n.a. PMID[14987050]
NPO33544 Lupinus formosus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15921409]
NPO11067 Buxus papillosa Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[20954721]
NPO12932 Hymenoclea salsola n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO11067 Buxus papillosa Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6806 Tyromyces fissilis Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11067 Buxus papillosa Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12932 Hymenoclea salsola n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO502 Sophora franchetiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12932 Hymenoclea salsola n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO308 Coelidium fourcadei n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12932 Hymenoclea salsola n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15990 Siphonaria diemenensis Species Siphonariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14350 Convallaria transcaucasica Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13873 Sphingobacterium multivorum Species Sphingobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7873 Artemisia sibirica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17555 Amphiporus angulatus Species Amphiporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO502 Sophora franchetiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11067 Buxus papillosa Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19041 Helichrysum albirosulatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17303 Valeriana fasciculata Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6806 Tyromyces fissilis Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18115 Aplophyllum vulcanicum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18162 Eranthemum pulchellum Species Acanthaceae 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
NPT32 Organism Mus musculus Mus musculus LD50 = 94.1 mg.kg-1 PMID[569839]

☑ 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 NPC76869 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 NPC477460
0.9194 High Similarity NPC477461
0.9194 High Similarity NPC477459
0.6667 Remote Similarity NPC57163
0.6667 Remote Similarity NPC267203
0.6667 Remote Similarity NPC132858
0.6667 Remote Similarity NPC77890
0.6667 Remote Similarity NPC116881
0.6625 Remote Similarity NPC308050
0.6463 Remote Similarity NPC127430
0.6463 Remote Similarity NPC120699
0.6463 Remote Similarity NPC268580
0.6437 Remote Similarity NPC43308
0.6389 Remote Similarity NPC470738
0.6351 Remote Similarity NPC206660
0.6296 Remote Similarity NPC320667
0.6296 Remote Similarity NPC214125
0.6279 Remote Similarity NPC135639
0.6279 Remote Similarity NPC143344
0.6279 Remote Similarity NPC61321
0.6279 Remote Similarity NPC78058
0.6279 Remote Similarity NPC234822
0.6173 Remote Similarity NPC63284
0.6164 Remote Similarity NPC42477
0.6092 Remote Similarity NPC207048
0.5833 Remote Similarity NPC25513
0.5833 Remote Similarity NPC86452
0.5833 Remote Similarity NPC244256
0.5806 Remote Similarity NPC167301
0.5778 Remote Similarity NPC476141
0.5682 Remote Similarity NPC215474
0.5658 Remote Similarity NPC252684
0.5638 Remote Similarity NPC145707
0.5625 Remote Similarity NPC471635
0.5625 Remote Similarity NPC25033
0.5625 Remote Similarity NPC119225
0.5625 Remote Similarity NPC470382
0.5625 Remote Similarity NPC476261
0.5604 Remote Similarity NPC157479

  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 NPC76869 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
0.6667 Remote Similarity NPD529 Approved
0.622 Remote Similarity NPD1426 Clinical (unspecified phase)
0.6145 Remote Similarity NPD1402 Approved
0.587 Remote Similarity NPD1691 Clinical (unspecified phase)
0.561 Remote Similarity NPD816 Approved
0.561 Remote Similarity NPD815 Approved
0.561 Remote Similarity NPD5365 Phase 2
0.5606 Remote Similarity NPD9674 Approved
0.5606 Remote Similarity NPD9675 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