Structure

Physi-Chem Properties

Molecular Weight:  627.58
Volume:  718.115
LogP:  10.662
LogD:  5.137
LogS:  -2.793
# Rotatable Bonds:  35
TPSA:  110.02
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.035
Synthetic Accessibility Score:  3.957
Fsp3:  0.974
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
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:  -5.421
MDCK Permeability:  5.426924872153904e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.753
Human Intestinal Absorption (HIA):  0.11
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  98.41344451904297%
Volume Distribution (VD):  0.829
Pgp-substrate:  1.5504076480865479%

ADMET: Metabolism

CYP1A2-inhibitor:  0.035
CYP1A2-substrate:  0.151
CYP2C19-inhibitor:  0.101
CYP2C19-substrate:  0.036
CYP2C9-inhibitor:  0.044
CYP2C9-substrate:  0.984
CYP2D6-inhibitor:  0.08
CYP2D6-substrate:  0.021
CYP3A4-inhibitor:  0.174
CYP3A4-substrate:  0.01

ADMET: Excretion

Clearance (CL):  4.245
Half-life (T1/2):  0.105

ADMET: Toxicity

hERG Blockers:  0.802
Human Hepatotoxicity (H-HT):  0.102
Drug-inuced Liver Injury (DILI):  0.023
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.055
Skin Sensitization:  0.95
Carcinogencity:  0.01
Eye Corrosion:  0.004
Eye Irritation:  0.026
Respiratory Toxicity:  0.928

Download Data

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

  Natural Product: NPC195165

Natural Product ID:  NPC195165
Common Name*:   (R)-2-Hydroxy-N-((2S,3S,4R)-1,3,4-Trihydroxy-14-Methylpentadecan-2-Yl)Docosanamide
IUPAC Name:   (2R)-2-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxy-14-methylpentadecan-2-yl]docosanamide
Synonyms:  
Standard InCHIKey:  MDBZNSRDVWLBHE-YUYNGSOASA-N
Standard InCHI:  InChI=1S/C38H77NO5/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-21-25-28-31-36(42)38(44)39-34(32-40)37(43)35(41)30-27-24-22-19-20-23-26-29-33(2)3/h33-37,40-43H,4-32H2,1-3H3,(H,39,44)/t34-,35+,36+,37-/m0/s1
SMILES:  CCCCCCCCCCCCCCCCCCCC[C@H](C(=N[C@H]([C@@H]([C@@H](CCCCCCCCCC(C)C)O)O)CO)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509564
PubChem CID:   10371786
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
NPO32609 cystodytes cf. dellechiajei Species Polycitoridae Eukaryota n.a. n.a. n.a. PMID[10869204]

☑ 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 ED50 = 100.0 ug ml-1 PMID[571570]

☑ 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 NPC195165 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
0.9538 High Similarity NPC477200
0.9194 High Similarity NPC145627
0.7949 Intermediate Similarity NPC477199
0.7949 Intermediate Similarity NPC476523
0.7941 Intermediate Similarity NPC474402
0.7903 Intermediate Similarity NPC270041
0.7703 Intermediate Similarity NPC217095
0.7703 Intermediate Similarity NPC264417
0.7333 Intermediate Similarity NPC86064
0.7297 Intermediate Similarity NPC474403
0.7273 Intermediate Similarity NPC8979
0.725 Intermediate Similarity NPC477730
0.72 Intermediate Similarity NPC43219
0.7164 Intermediate Similarity NPC472578
0.7143 Intermediate Similarity NPC470284
0.7042 Intermediate Similarity NPC41429
0.6962 Remote Similarity NPC478017
0.6962 Remote Similarity NPC315131
0.6962 Remote Similarity NPC315535
0.6935 Remote Similarity NPC319709
0.6935 Remote Similarity NPC289484
0.6905 Remote Similarity NPC477728
0.6883 Remote Similarity NPC288086
0.6875 Remote Similarity NPC326283
0.6875 Remote Similarity NPC321394
0.6867 Remote Similarity NPC227051
0.6835 Remote Similarity NPC316242
0.679 Remote Similarity NPC314466
0.6757 Remote Similarity NPC470110
0.675 Remote Similarity NPC473984
0.6747 Remote Similarity NPC145748
0.6747 Remote Similarity NPC155670
0.6747 Remote Similarity NPC95478
0.6742 Remote Similarity NPC470283
0.6719 Remote Similarity NPC80350
0.6667 Remote Similarity NPC477729
0.6667 Remote Similarity NPC123814
0.6667 Remote Similarity NPC137327
0.6622 Remote Similarity NPC470109
0.6596 Remote Similarity NPC477198
0.6579 Remote Similarity NPC478256
0.6579 Remote Similarity NPC476285
0.6528 Remote Similarity NPC17455
0.6517 Remote Similarity NPC270005
0.6517 Remote Similarity NPC208537
0.6494 Remote Similarity NPC476695
0.6494 Remote Similarity NPC476696
0.6494 Remote Similarity NPC476694
0.6486 Remote Similarity NPC470108
0.6486 Remote Similarity NPC238646
0.6447 Remote Similarity NPC474299
0.6447 Remote Similarity NPC28348
0.6447 Remote Similarity NPC473985
0.6447 Remote Similarity NPC474298
0.6447 Remote Similarity NPC475808
0.6438 Remote Similarity NPC471419
0.6438 Remote Similarity NPC163134
0.6418 Remote Similarity NPC474322
0.6413 Remote Similarity NPC313821
0.6413 Remote Similarity NPC189629
0.6386 Remote Similarity NPC207657
0.6375 Remote Similarity NPC476324
0.6375 Remote Similarity NPC476130
0.6364 Remote Similarity NPC103712
0.6364 Remote Similarity NPC291196
0.6364 Remote Similarity NPC476291
0.6333 Remote Similarity NPC475603
0.6333 Remote Similarity NPC61894
0.6329 Remote Similarity NPC138435
0.6316 Remote Similarity NPC306763
0.6316 Remote Similarity NPC266242
0.6316 Remote Similarity NPC74555
0.6316 Remote Similarity NPC254617
0.625 Remote Similarity NPC470282
0.625 Remote Similarity NPC319131
0.6234 Remote Similarity NPC475127
0.6234 Remote Similarity NPC472579
0.6234 Remote Similarity NPC473419
0.6234 Remote Similarity NPC268922
0.6234 Remote Similarity NPC475715
0.6211 Remote Similarity NPC271207
0.6211 Remote Similarity NPC206711
0.6211 Remote Similarity NPC225978
0.6211 Remote Similarity NPC255175
0.6203 Remote Similarity NPC141325
0.6203 Remote Similarity NPC474468
0.6197 Remote Similarity NPC328447
0.6184 Remote Similarity NPC59221
0.6184 Remote Similarity NPC184150
0.6184 Remote Similarity NPC141156
0.6163 Remote Similarity NPC320936
0.6163 Remote Similarity NPC228638
0.6154 Remote Similarity NPC223174
0.6154 Remote Similarity NPC327753
0.6154 Remote Similarity NPC473710
0.6154 Remote Similarity NPC475694
0.6154 Remote Similarity NPC163538
0.6154 Remote Similarity NPC115800
0.6154 Remote Similarity NPC327486
0.6145 Remote Similarity NPC474833
0.6129 Remote Similarity NPC241279
0.6119 Remote Similarity NPC224624
0.6111 Remote Similarity NPC39290
0.6111 Remote Similarity NPC159369
0.6104 Remote Similarity NPC474469
0.6104 Remote Similarity NPC471418
0.6098 Remote Similarity NPC472594
0.6082 Remote Similarity NPC314387
0.6061 Remote Similarity NPC96966
0.6061 Remote Similarity NPC87359
0.6061 Remote Similarity NPC29222
0.6061 Remote Similarity NPC121062
0.6061 Remote Similarity NPC180402
0.6053 Remote Similarity NPC294883
0.6053 Remote Similarity NPC12514
0.6049 Remote Similarity NPC472595
0.6026 Remote Similarity NPC193280
0.6026 Remote Similarity NPC314273
0.6024 Remote Similarity NPC37681
0.6 Remote Similarity NPC316186
0.6 Remote Similarity NPC471917
0.5978 Remote Similarity NPC315237
0.5976 Remote Similarity NPC477002
0.5972 Remote Similarity NPC322148
0.5952 Remote Similarity NPC316807
0.593 Remote Similarity NPC192456
0.5926 Remote Similarity NPC476248
0.5921 Remote Similarity NPC474928
0.5921 Remote Similarity NPC233034
0.5897 Remote Similarity NPC34291
0.5897 Remote Similarity NPC126664
0.5895 Remote Similarity NPC47076
0.5895 Remote Similarity NPC134504
0.589 Remote Similarity NPC476537
0.589 Remote Similarity NPC471421
0.589 Remote Similarity NPC233364
0.589 Remote Similarity NPC170172
0.589 Remote Similarity NPC216415
0.5882 Remote Similarity NPC319110
0.5882 Remote Similarity NPC329181
0.5862 Remote Similarity NPC47135
0.5851 Remote Similarity NPC256570
0.5851 Remote Similarity NPC192066
0.5851 Remote Similarity NPC3568
0.5851 Remote Similarity NPC17290
0.5844 Remote Similarity NPC286851
0.5844 Remote Similarity NPC303798
0.5833 Remote Similarity NPC471443
0.5833 Remote Similarity NPC471605
0.5823 Remote Similarity NPC474812
0.5811 Remote Similarity NPC326524
0.5811 Remote Similarity NPC328786
0.5811 Remote Similarity NPC325550
0.5811 Remote Similarity NPC201338
0.5811 Remote Similarity NPC329003
0.5811 Remote Similarity NPC474627
0.5806 Remote Similarity NPC111567
0.5806 Remote Similarity NPC309898
0.5806 Remote Similarity NPC473581
0.5806 Remote Similarity NPC186840
0.5806 Remote Similarity NPC473604
0.5806 Remote Similarity NPC263545
0.5806 Remote Similarity NPC473950
0.5806 Remote Similarity NPC475125
0.5806 Remote Similarity NPC15851
0.5795 Remote Similarity NPC323180
0.5783 Remote Similarity NPC62293
0.5783 Remote Similarity NPC51055
0.5783 Remote Similarity NPC140327
0.5783 Remote Similarity NPC212008
0.5773 Remote Similarity NPC220234
0.5765 Remote Similarity NPC469492
0.5747 Remote Similarity NPC109533
0.5747 Remote Similarity NPC82799
0.5743 Remote Similarity NPC475918
0.5733 Remote Similarity NPC112398
0.5732 Remote Similarity NPC314678
0.573 Remote Similarity NPC175419
0.5729 Remote Similarity NPC475503
0.5729 Remote Similarity NPC8098
0.5729 Remote Similarity NPC197294
0.5729 Remote Similarity NPC183449
0.5714 Remote Similarity NPC471892
0.5714 Remote Similarity NPC223386
0.5714 Remote Similarity NPC75435
0.5714 Remote Similarity NPC471780
0.5714 Remote Similarity NPC142290
0.5714 Remote Similarity NPC198341
0.5701 Remote Similarity NPC296043
0.57 Remote Similarity NPC476877
0.5699 Remote Similarity NPC242503
0.5699 Remote Similarity NPC139782
0.5699 Remote Similarity NPC74672
0.5699 Remote Similarity NPC43074
0.5699 Remote Similarity NPC209047
0.5698 Remote Similarity NPC469517
0.5684 Remote Similarity NPC158445
0.5684 Remote Similarity NPC23454
0.5684 Remote Similarity NPC282088
0.5684 Remote Similarity NPC35269

  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 NPC195165 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
0.8551 High Similarity NPD3187 Discontinued
0.7536 Intermediate Similarity NPD1831 Phase 3
0.6962 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6962 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6935 Remote Similarity NPD3211 Approved
0.6875 Remote Similarity NPD9678 Approved
0.6875 Remote Similarity NPD9677 Phase 3
0.6667 Remote Similarity NPD3215 Phase 1
0.6508 Remote Similarity NPD1152 Phase 2
0.6413 Remote Similarity NPD3191 Approved
0.6413 Remote Similarity NPD3190 Approved
0.6413 Remote Similarity NPD3189 Approved
0.64 Remote Similarity NPD2263 Discontinued
0.6364 Remote Similarity NPD3214 Discontinued
0.6301 Remote Similarity NPD5375 Phase 3
0.6296 Remote Similarity NPD2689 Clinical (unspecified phase)
0.6263 Remote Similarity NPD8174 Phase 2
0.6234 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6232 Remote Similarity NPD1830 Clinical (unspecified phase)
0.6207 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6197 Remote Similarity NPD9661 Approved
0.6196 Remote Similarity NPD8394 Approved
0.6184 Remote Similarity NPD5380 Approved
0.6173 Remote Similarity NPD1453 Phase 1
0.6164 Remote Similarity NPD393 Approved
0.6154 Remote Similarity NPD9445 Approved
0.6129 Remote Similarity NPD7844 Discontinued
0.6082 Remote Similarity NPD3185 Approved
0.6082 Remote Similarity NPD3183 Approved
0.6082 Remote Similarity NPD3184 Approved
0.6082 Remote Similarity NPD3182 Approved
0.6076 Remote Similarity NPD9446 Approved
0.6027 Remote Similarity NPD9455 Approved
0.5921 Remote Similarity NPD9440 Discontinued
0.5909 Remote Similarity NPD379 Clinical (unspecified phase)
0.5897 Remote Similarity NPD9444 Discontinued
0.5897 Remote Similarity NPD9443 Clinical (unspecified phase)
0.5862 Remote Similarity NPD7345 Approved
0.5843 Remote Similarity NPD619 Phase 3
0.5761 Remote Similarity NPD3716 Discontinued
0.575 Remote Similarity NPD2702 Phase 1
0.575 Remote Similarity NPD2704 Phase 3
0.5747 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5728 Remote Similarity NPD8305 Approved
0.5728 Remote Similarity NPD8306 Approved
0.5699 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5673 Remote Similarity NPD3188 Approved
0.5652 Remote Similarity NPD618 Clinical (unspecified phase)
0.5652 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5647 Remote Similarity NPD3160 Suspended
0.561 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5607 Remote Similarity NPD7916 Approved
0.5607 Remote Similarity NPD7915 Approved
0.56 Remote Similarity NPD9239 Approved
0.56 Remote Similarity NPD9240 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