Structure

Physi-Chem Properties

Molecular Weight:  196.18
Volume:  236.922
LogP:  4.842
LogD:  3.629
LogS:  -4.117
# Rotatable Bonds:  10
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.29
Synthetic Accessibility Score:  2.202
Fsp3:  0.769
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.559
MDCK Permeability:  2.6614741727826186e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.81
30% Bioavailability (F30%):  0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.965
Plasma Protein Binding (PPB):  94.2470932006836%
Volume Distribution (VD):  1.094
Pgp-substrate:  3.853864908218384%

ADMET: Metabolism

CYP1A2-inhibitor:  0.94
CYP1A2-substrate:  0.372
CYP2C19-inhibitor:  0.751
CYP2C19-substrate:  0.48
CYP2C9-inhibitor:  0.464
CYP2C9-substrate:  0.974
CYP2D6-inhibitor:  0.151
CYP2D6-substrate:  0.754
CYP3A4-inhibitor:  0.252
CYP3A4-substrate:  0.104

ADMET: Excretion

Clearance (CL):  2.609
Half-life (T1/2):  0.291

ADMET: Toxicity

hERG Blockers:  0.084
Human Hepatotoxicity (H-HT):  0.036
Drug-inuced Liver Injury (DILI):  0.109
AMES Toxicity:  0.391
Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.056
Skin Sensitization:  0.962
Carcinogencity:  0.387
Eye Corrosion:  0.984
Eye Irritation:  0.975
Respiratory Toxicity:  0.955

Download Data

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

  Natural Product: NPC298710

Natural Product ID:  NPC298710
Common Name*:   (E)-Tridec-2-Enal
IUPAC Name:   (E)-tridec-2-enal
Synonyms:  
Standard InCHIKey:  VMUNAKQXJLHODT-VAWYXSNFSA-N
Standard InCHI:  InChI=1S/C13H24O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14/h11-13H,2-10H2,1H3/b12-11+
SMILES:  CCCCCCCCCC/C=C/C=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1995395
PubChem CID:   5283363
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000298] Fatty aldehydes

*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
NPO8952 Craibiodendron yunnanese Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8952 Craibiodendron yunnanese Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

☑ 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
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT369 Cell Line ACHN Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT116 Cell Line HL-60 Homo sapiens GI50 n.a. 56104.8 nM PMID[506384]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT374 Cell Line SF-539 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT373 Cell Line SK-MEL-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT376 Cell Line A498 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT111 Cell Line K562 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT112 Cell Line MOLT-4 Homo sapiens GI50 n.a. 70307.23 nM PMID[506384]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT382 Cell Line OVCAR-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT572 Cell Line DMS-273 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT385 Cell Line SR Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT384 Cell Line TK-10 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT323 Cell Line SW-620 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT573 Cell Line M19-MEL Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT455 Cell Line NCI-H522 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT387 Cell Line M14 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT574 Cell Line XF498 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT575 Cell Line KM-20L2 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT731 Cell Line LXFL 529 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT576 Cell Line DMS-114 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT577 Cell Line RXF 631 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT578 Cell Line SNB-78 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT579 Cell Line DLD-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT170 Cell Line SK-MEL-28 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT139 Cell Line HT-29 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT406 Cell Line RXF 393 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT732 Cell Line HOP-18 Homo sapiens GI50 n.a. 100000.0 nM PMID[506384]
NPT593 Organism Bursaphelenchus xylophilus Bursaphelenchus xylophilus mortality = 4.9 % PMID[506385]

☑ 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 NPC298710 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 NPC67920
1.0 High Similarity NPC287397
0.9744 High Similarity NPC33489
0.9231 High Similarity NPC33761
0.9024 High Similarity NPC208936
0.8718 High Similarity NPC279300
0.8537 High Similarity NPC18205
0.8537 High Similarity NPC12319
0.8537 High Similarity NPC323278
0.8462 Intermediate Similarity NPC75204
0.8293 Intermediate Similarity NPC217923
0.8205 Intermediate Similarity NPC72258
0.8043 Intermediate Similarity NPC324812
0.8 Intermediate Similarity NPC239754
0.7917 Intermediate Similarity NPC234829
0.7826 Intermediate Similarity NPC110234
0.7826 Intermediate Similarity NPC44363
0.7826 Intermediate Similarity NPC163751
0.7805 Intermediate Similarity NPC8416
0.7778 Intermediate Similarity NPC145755
0.7778 Intermediate Similarity NPC267514
0.7674 Intermediate Similarity NPC101147
0.75 Intermediate Similarity NPC270170
0.75 Intermediate Similarity NPC7754
0.75 Intermediate Similarity NPC477789
0.7381 Intermediate Similarity NPC254764
0.7358 Intermediate Similarity NPC281986
0.7358 Intermediate Similarity NPC22019
0.7358 Intermediate Similarity NPC321568
0.7358 Intermediate Similarity NPC208749
0.7308 Intermediate Similarity NPC317899
0.7273 Intermediate Similarity NPC48930
0.7083 Intermediate Similarity NPC100380
0.7073 Intermediate Similarity NPC146507
0.6981 Remote Similarity NPC188789
0.6939 Remote Similarity NPC471958
0.6923 Remote Similarity NPC8466
0.6875 Remote Similarity NPC474362
0.6875 Remote Similarity NPC474202
0.6829 Remote Similarity NPC144407
0.6818 Remote Similarity NPC92863
0.6818 Remote Similarity NPC155880
0.6809 Remote Similarity NPC216921
0.6809 Remote Similarity NPC301972
0.6809 Remote Similarity NPC106819
0.6809 Remote Similarity NPC252978
0.68 Remote Similarity NPC207815
0.68 Remote Similarity NPC145311
0.6792 Remote Similarity NPC100809
0.6792 Remote Similarity NPC209431
0.6735 Remote Similarity NPC195246
0.6735 Remote Similarity NPC22098
0.6735 Remote Similarity NPC276009
0.6667 Remote Similarity NPC474391
0.6667 Remote Similarity NPC108195
0.6667 Remote Similarity NPC288381
0.6667 Remote Similarity NPC471239
0.6667 Remote Similarity NPC310810
0.6667 Remote Similarity NPC15934
0.6667 Remote Similarity NPC20934
0.6596 Remote Similarity NPC149668
0.6585 Remote Similarity NPC273054
0.6585 Remote Similarity NPC151719
0.6538 Remote Similarity NPC477458
0.6538 Remote Similarity NPC30433
0.6531 Remote Similarity NPC191337
0.6531 Remote Similarity NPC269074
0.6531 Remote Similarity NPC76976
0.6522 Remote Similarity NPC113082
0.6491 Remote Similarity NPC159650
0.6491 Remote Similarity NPC22897
0.6444 Remote Similarity NPC40434
0.6444 Remote Similarity NPC34873
0.6429 Remote Similarity NPC109034
0.64 Remote Similarity NPC55063
0.64 Remote Similarity NPC19834
0.64 Remote Similarity NPC262558
0.64 Remote Similarity NPC8610
0.6379 Remote Similarity NPC143857
0.6379 Remote Similarity NPC229252
0.6346 Remote Similarity NPC236338
0.6346 Remote Similarity NPC15325
0.6333 Remote Similarity NPC52449
0.6333 Remote Similarity NPC169275
0.6327 Remote Similarity NPC25771
0.6327 Remote Similarity NPC114841
0.6327 Remote Similarity NPC477686
0.6296 Remote Similarity NPC69898
0.6296 Remote Similarity NPC14002
0.6296 Remote Similarity NPC295777
0.6296 Remote Similarity NPC296311
0.6279 Remote Similarity NPC12889
0.6271 Remote Similarity NPC294304
0.6271 Remote Similarity NPC228574
0.625 Remote Similarity NPC472808
0.625 Remote Similarity NPC324224
0.625 Remote Similarity NPC304151
0.623 Remote Similarity NPC183422
0.6222 Remote Similarity NPC24833
0.6222 Remote Similarity NPC185839
0.6222 Remote Similarity NPC220061
0.6222 Remote Similarity NPC216416
0.6207 Remote Similarity NPC82465
0.62 Remote Similarity NPC270706
0.62 Remote Similarity NPC276825
0.6182 Remote Similarity NPC269615
0.6182 Remote Similarity NPC5626
0.6182 Remote Similarity NPC189677
0.6182 Remote Similarity NPC137538
0.6182 Remote Similarity NPC300121
0.6182 Remote Similarity NPC250539
0.6182 Remote Similarity NPC478120
0.617 Remote Similarity NPC329762
0.617 Remote Similarity NPC123357
0.617 Remote Similarity NPC111474
0.617 Remote Similarity NPC27444
0.617 Remote Similarity NPC103236
0.6167 Remote Similarity NPC179087
0.6167 Remote Similarity NPC210303
0.6167 Remote Similarity NPC44343
0.6154 Remote Similarity NPC85079
0.6154 Remote Similarity NPC266539
0.6154 Remote Similarity NPC287191
0.6154 Remote Similarity NPC266144
0.6154 Remote Similarity NPC98284
0.6154 Remote Similarity NPC31891
0.6154 Remote Similarity NPC248884
0.6154 Remote Similarity NPC31194
0.6136 Remote Similarity NPC182392
0.6136 Remote Similarity NPC269641
0.6122 Remote Similarity NPC292463
0.6111 Remote Similarity NPC106531
0.6098 Remote Similarity NPC34671
0.6087 Remote Similarity NPC226511
0.6087 Remote Similarity NPC180840
0.6078 Remote Similarity NPC471752
0.6078 Remote Similarity NPC180575
0.6078 Remote Similarity NPC128280
0.6071 Remote Similarity NPC223677
0.6071 Remote Similarity NPC28779
0.6071 Remote Similarity NPC128061
0.6071 Remote Similarity NPC52264
0.6071 Remote Similarity NPC200845
0.6071 Remote Similarity NPC10316
0.6047 Remote Similarity NPC266979
0.6042 Remote Similarity NPC221250
0.6042 Remote Similarity NPC469713
0.6038 Remote Similarity NPC118788
0.6038 Remote Similarity NPC163984
0.6038 Remote Similarity NPC224227
0.6038 Remote Similarity NPC176819
0.6038 Remote Similarity NPC474642
0.6038 Remote Similarity NPC58970
0.6038 Remote Similarity NPC59051
0.6038 Remote Similarity NPC15789
0.6038 Remote Similarity NPC32351
0.6038 Remote Similarity NPC249670
0.6038 Remote Similarity NPC228776
0.6038 Remote Similarity NPC72699
0.6038 Remote Similarity NPC473913
0.6038 Remote Similarity NPC225974
0.6034 Remote Similarity NPC21946
0.6034 Remote Similarity NPC60772
0.6032 Remote Similarity NPC290350
0.6032 Remote Similarity NPC4370
0.6 Remote Similarity NPC139545
0.6 Remote Similarity NPC38497
0.6 Remote Similarity NPC213767
0.6 Remote Similarity NPC61177
0.6 Remote Similarity NPC284224
0.6 Remote Similarity NPC304079
0.6 Remote Similarity NPC23117
0.6 Remote Similarity NPC6963
0.6 Remote Similarity NPC101616
0.6 Remote Similarity NPC12907
0.6 Remote Similarity NPC471753
0.6 Remote Similarity NPC71761
0.6 Remote Similarity NPC168407
0.6 Remote Similarity NPC260573
0.6 Remote Similarity NPC39633
0.6 Remote Similarity NPC37644
0.6 Remote Similarity NPC309606
0.5968 Remote Similarity NPC296436
0.5968 Remote Similarity NPC176215
0.5965 Remote Similarity NPC245002
0.5965 Remote Similarity NPC325977
0.5965 Remote Similarity NPC477790
0.5957 Remote Similarity NPC171978
0.5957 Remote Similarity NPC277382
0.5957 Remote Similarity NPC255042
0.5957 Remote Similarity NPC29091
0.5957 Remote Similarity NPC103213
0.5957 Remote Similarity NPC182840
0.5938 Remote Similarity NPC155198
0.5932 Remote Similarity NPC106851
0.5932 Remote Similarity NPC274927
0.5926 Remote Similarity NPC151782
0.5926 Remote Similarity NPC262968
0.5918 Remote Similarity NPC57923
0.5918 Remote Similarity NPC187922

  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 NPC298710 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
0.6 Remote Similarity NPD6097 Approved
0.6 Remote Similarity NPD6096 Approved
0.5962 Remote Similarity NPD5343 Approved
0.5957 Remote Similarity NPD5783 Phase 3
0.5926 Remote Similarity NPD28 Approved
0.5926 Remote Similarity NPD29 Approved
0.5882 Remote Similarity NPD3174 Discontinued
0.5882 Remote Similarity NPD39 Approved
0.5849 Remote Similarity NPD4220 Pre-registration
0.5714 Remote Similarity NPD3172 Approved
0.5625 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5614 Remote Similarity NPD3195 Phase 2
0.5614 Remote Similarity NPD4266 Approved
0.5614 Remote Similarity NPD3194 Approved
0.5614 Remote Similarity NPD3196 Approved
0.56 Remote Similarity NPD9297 Discontinued
0.56 Remote Similarity NPD9091 Suspended

  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