Structure

Physi-Chem Properties

Molecular Weight:  681.63
Volume:  784.663
LogP:  12.168
LogD:  5.392
LogS:  -2.084
# Rotatable Bonds:  39
TPSA:  110.02
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.033
Synthetic Accessibility Score:  3.916
Fsp3:  0.929
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.353
MDCK Permeability:  2.9301918402779847e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.253
Human Intestinal Absorption (HIA):  0.132
20% Bioavailability (F20%):  0.923
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  101.62223052978516%
Volume Distribution (VD):  0.838
Pgp-substrate:  0.7089117169380188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.028
CYP1A2-substrate:  0.125
CYP2C19-inhibitor:  0.092
CYP2C19-substrate:  0.033
CYP2C9-inhibitor:  0.036
CYP2C9-substrate:  0.995
CYP2D6-inhibitor:  0.204
CYP2D6-substrate:  0.02
CYP3A4-inhibitor:  0.187
CYP3A4-substrate:  0.005

ADMET: Excretion

Clearance (CL):  3.283
Half-life (T1/2):  0.126

ADMET: Toxicity

hERG Blockers:  0.794
Human Hepatotoxicity (H-HT):  0.035
Drug-inuced Liver Injury (DILI):  0.016
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.965
Carcinogencity:  0.006
Eye Corrosion:  0.004
Eye Irritation:  0.291
Respiratory Toxicity:  0.765

Download Data

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

  Natural Product: NPC264417

Natural Product ID:  NPC264417
Common Name*:   Benjaminamide
IUPAC Name:   (2R)-2-hydroxy-N-[(E,2S,3S,4R)-1,3,4-trihydroxyoctadec-12-en-2-yl]tetracosanamide
Synonyms:   Benjaminamide
Standard InCHIKey:  SOZSUYGVBDXLLZ-HSMPPUOJSA-N
Standard InCHI:  InChI=1S/C42H83NO5/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-40(46)42(48)43-38(37-44)41(47)39(45)35-33-31-29-27-25-16-14-12-10-8-6-4-2/h12,14,38-41,44-47H,3-11,13,15-37H2,1-2H3,(H,43,48)/b14-12+/t38-,39+,40+,41-/m0/s1
SMILES:  CCCCCCCCCCCCCCCCCCCCCC[C@H](C(=N[C@H]([C@@H]([C@@H](CCCCCCC/C=C/CCCCC)O)O)CO)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1812594
PubChem CID:   56662789
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000257] Sphingolipids
        • [CHEMONTID:0001418] Ceramides
          • [CHEMONTID:0002963] Phytoceramides

*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
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. fruit n.a. PMID[21619045]
NPO13906 Ficus mucuso Species Moraceae Eukaryota figs Tongolo-Yaound, in the Central Region of Cameroon 2008-JUN PMID[21619045]
NPO10164 Convolvulus scammonia Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10164 Convolvulus scammonia Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10164 Convolvulus scammonia Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10164 Convolvulus scammonia Species Convolvulaceae 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
NPT2 Others Unspecified Inhibition = 1.7 % PMID[478350]

☑ 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 NPC264417 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 NPC217095
0.9028 High Similarity NPC288086
0.8846 High Similarity NPC477199
0.8472 Intermediate Similarity NPC103712
0.8472 Intermediate Similarity NPC291196
0.8261 Intermediate Similarity NPC145627
0.8118 Intermediate Similarity NPC61894
0.8118 Intermediate Similarity NPC475603
0.8077 Intermediate Similarity NPC474833
0.7971 Intermediate Similarity NPC329003
0.7971 Intermediate Similarity NPC325550
0.7971 Intermediate Similarity NPC326524
0.7882 Intermediate Similarity NPC159369
0.7882 Intermediate Similarity NPC39290
0.7826 Intermediate Similarity NPC321030
0.7703 Intermediate Similarity NPC195165
0.7692 Intermediate Similarity NPC62293
0.7692 Intermediate Similarity NPC212008
0.7692 Intermediate Similarity NPC51055
0.7692 Intermediate Similarity NPC140327
0.759 Intermediate Similarity NPC228638
0.7561 Intermediate Similarity NPC82799
0.75 Intermediate Similarity NPC263545
0.75 Intermediate Similarity NPC475125
0.75 Intermediate Similarity NPC473581
0.75 Intermediate Similarity NPC473950
0.75 Intermediate Similarity NPC309898
0.75 Intermediate Similarity NPC186840
0.75 Intermediate Similarity NPC15851
0.75 Intermediate Similarity NPC473604
0.75 Intermediate Similarity NPC111567
0.7468 Intermediate Similarity NPC3094
0.7436 Intermediate Similarity NPC314678
0.7403 Intermediate Similarity NPC477200
0.7391 Intermediate Similarity NPC242930
0.7386 Intermediate Similarity NPC209047
0.7386 Intermediate Similarity NPC43074
0.7386 Intermediate Similarity NPC139782
0.7386 Intermediate Similarity NPC242503
0.7386 Intermediate Similarity NPC74672
0.734 Intermediate Similarity NPC477198
0.7333 Intermediate Similarity NPC158445
0.7333 Intermediate Similarity NPC256570
0.7333 Intermediate Similarity NPC156782
0.7333 Intermediate Similarity NPC282088
0.7333 Intermediate Similarity NPC54961
0.7333 Intermediate Similarity NPC157353
0.7333 Intermediate Similarity NPC3568
0.7333 Intermediate Similarity NPC192066
0.7333 Intermediate Similarity NPC113224
0.7333 Intermediate Similarity NPC17290
0.7303 Intermediate Similarity NPC182632
0.7303 Intermediate Similarity NPC282705
0.7262 Intermediate Similarity NPC474312
0.726 Intermediate Similarity NPC47333
0.7229 Intermediate Similarity NPC207657
0.7174 Intermediate Similarity NPC197294
0.7174 Intermediate Similarity NPC183449
0.7174 Intermediate Similarity NPC8098
0.7162 Intermediate Similarity NPC477106
0.7143 Intermediate Similarity NPC70323
0.7143 Intermediate Similarity NPC23454
0.7143 Intermediate Similarity NPC262312
0.7143 Intermediate Similarity NPC474812
0.7143 Intermediate Similarity NPC35269
0.7101 Intermediate Similarity NPC270041
0.7024 Intermediate Similarity NPC79367
0.6989 Remote Similarity NPC45313
0.6933 Remote Similarity NPC316674
0.6837 Remote Similarity NPC74035
0.68 Remote Similarity NPC29468
0.679 Remote Similarity NPC305223
0.6778 Remote Similarity NPC316186
0.6768 Remote Similarity NPC475918
0.6753 Remote Similarity NPC477525
0.6712 Remote Similarity NPC168308
0.6712 Remote Similarity NPC302569
0.6711 Remote Similarity NPC55068
0.6667 Remote Similarity NPC129995
0.6667 Remote Similarity NPC130807
0.6667 Remote Similarity NPC315141
0.6588 Remote Similarity NPC475363
0.6588 Remote Similarity NPC473971
0.6588 Remote Similarity NPC473972
0.6575 Remote Similarity NPC8979
0.6566 Remote Similarity NPC476877
0.6494 Remote Similarity NPC471023
0.6479 Remote Similarity NPC188341
0.6479 Remote Similarity NPC49494
0.6458 Remote Similarity NPC475503
0.6436 Remote Similarity NPC201128
0.6436 Remote Similarity NPC476876
0.642 Remote Similarity NPC127145
0.642 Remote Similarity NPC475930
0.641 Remote Similarity NPC235311
0.641 Remote Similarity NPC253468
0.64 Remote Similarity NPC325734
0.6392 Remote Similarity NPC475646
0.6341 Remote Similarity NPC474674
0.6341 Remote Similarity NPC324638
0.6338 Remote Similarity NPC261571
0.6337 Remote Similarity NPC194390
0.6337 Remote Similarity NPC88267
0.6337 Remote Similarity NPC113326
0.6337 Remote Similarity NPC224610
0.6333 Remote Similarity NPC476523
0.6329 Remote Similarity NPC474402
0.6322 Remote Similarity NPC477485
0.6296 Remote Similarity NPC23721
0.6289 Remote Similarity NPC189629
0.6289 Remote Similarity NPC175614
0.6267 Remote Similarity NPC52012
0.6235 Remote Similarity NPC476924
0.6232 Remote Similarity NPC289484
0.6232 Remote Similarity NPC319709
0.622 Remote Similarity NPC137620
0.622 Remote Similarity NPC474675
0.6196 Remote Similarity NPC258824
0.6164 Remote Similarity NPC477724
0.6164 Remote Similarity NPC26102
0.6164 Remote Similarity NPC187361
0.6154 Remote Similarity NPC321838
0.6136 Remote Similarity NPC314762
0.6132 Remote Similarity NPC29501
0.6132 Remote Similarity NPC476875
0.6118 Remote Similarity NPC470992
0.6118 Remote Similarity NPC470993
0.6104 Remote Similarity NPC312826
0.61 Remote Similarity NPC206711
0.61 Remote Similarity NPC271207
0.61 Remote Similarity NPC255175
0.61 Remote Similarity NPC233932
0.61 Remote Similarity NPC225978
0.6098 Remote Similarity NPC141481
0.6098 Remote Similarity NPC324981
0.6098 Remote Similarity NPC48218
0.6098 Remote Similarity NPC473559
0.6092 Remote Similarity NPC477484
0.6092 Remote Similarity NPC477486
0.6087 Remote Similarity NPC76976
0.6064 Remote Similarity NPC34754
0.6053 Remote Similarity NPC470970
0.6044 Remote Similarity NPC178758
0.6044 Remote Similarity NPC196102
0.6042 Remote Similarity NPC319473
0.6038 Remote Similarity NPC251122
0.6038 Remote Similarity NPC113012
0.6038 Remote Similarity NPC122926
0.6027 Remote Similarity NPC123814
0.6024 Remote Similarity NPC280065
0.6024 Remote Similarity NPC471022
0.6024 Remote Similarity NPC45060
0.6023 Remote Similarity NPC469492
0.6018 Remote Similarity NPC273185
0.6 Remote Similarity NPC281590
0.6 Remote Similarity NPC26932
0.6 Remote Similarity NPC55652
0.5976 Remote Similarity NPC330426
0.5976 Remote Similarity NPC22101
0.5976 Remote Similarity NPC473829
0.5976 Remote Similarity NPC475443
0.5976 Remote Similarity NPC148192
0.5976 Remote Similarity NPC271921
0.5976 Remote Similarity NPC104537
0.5976 Remote Similarity NPC127091
0.5962 Remote Similarity NPC258130
0.5955 Remote Similarity NPC469517
0.5952 Remote Similarity NPC476660
0.5952 Remote Similarity NPC97614
0.5952 Remote Similarity NPC476696
0.5952 Remote Similarity NPC476694
0.5952 Remote Similarity NPC476695
0.5949 Remote Similarity NPC17455
0.5946 Remote Similarity NPC474496
0.5934 Remote Similarity NPC469833
0.5934 Remote Similarity NPC469838
0.5934 Remote Similarity NPC39966
0.5934 Remote Similarity NPC477730
0.593 Remote Similarity NPC78562
0.593 Remote Similarity NPC473588
0.5921 Remote Similarity NPC471960
0.5921 Remote Similarity NPC475384
0.5921 Remote Similarity NPC161838
0.5921 Remote Similarity NPC470966
0.5921 Remote Similarity NPC477661
0.5921 Remote Similarity NPC470968
0.5921 Remote Similarity NPC470967
0.5921 Remote Similarity NPC473847
0.5921 Remote Similarity NPC470969
0.5909 Remote Similarity NPC325936
0.5909 Remote Similarity NPC274293
0.5909 Remote Similarity NPC172197
0.5905 Remote Similarity NPC475800
0.5904 Remote Similarity NPC249713
0.5904 Remote Similarity NPC474298
0.5904 Remote Similarity NPC473985
0.5904 Remote Similarity NPC475808
0.5904 Remote Similarity NPC474299
0.5904 Remote Similarity NPC28348
0.59 Remote Similarity NPC240650

  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 NPC264417 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
0.7386 Intermediate Similarity NPD8522 Clinical (unspecified phase)
0.6875 Remote Similarity NPD3187 Discontinued
0.6711 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6346 Remote Similarity NPD6421 Discontinued
0.6341 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6316 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6232 Remote Similarity NPD3211 Approved
0.6154 Remote Similarity NPD6949 Clinical (unspecified phase)
0.6027 Remote Similarity NPD3215 Phase 1
0.6 Remote Similarity NPD1831 Phase 3
0.5977 Remote Similarity NPD818 Approved
0.5977 Remote Similarity NPD819 Approved
0.5857 Remote Similarity NPD1152 Phase 2
0.581 Remote Similarity NPD5357 Phase 1
0.5802 Remote Similarity NPD3197 Phase 1
0.58 Remote Similarity NPD4228 Discovery
0.5758 Remote Similarity NPD8394 Approved
0.5753 Remote Similarity NPD3214 Discontinued
0.5753 Remote Similarity NPD9678 Approved
0.5753 Remote Similarity NPD9677 Phase 3
0.5741 Remote Similarity NPD6420 Discontinued
0.5714 Remote Similarity NPD6935 Phase 3
0.5714 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5702 Remote Similarity NPD2217 Approved
0.5702 Remote Similarity NPD2218 Phase 2
0.5673 Remote Similarity NPD244 Clinical (unspecified phase)
0.5667 Remote Similarity NPD3732 Approved
0.5663 Remote Similarity NPD5380 Approved
0.5647 Remote Similarity NPD9445 Approved
0.5625 Remote Similarity NPD393 Approved
0.5619 Remote Similarity NPD1407 Approved
0.5612 Remote Similarity NPD6943 Clinical (unspecified phase)
0.561 Remote Similarity NPD277 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