Structure

Physi-Chem Properties

Molecular Weight:  272.24
Volume:  309.026
LogP:  5.509
LogD:  2.594
LogS:  -4.614
# Rotatable Bonds:  14
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.457
Synthetic Accessibility Score:  2.37
Fsp3:  0.938
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.042
MDCK Permeability:  4.27413651777897e-05
Pgp-inhibitor:  0.02
Pgp-substrate:  0.115
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.85
30% Bioavailability (F30%):  0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.547
Plasma Protein Binding (PPB):  96.94429779052734%
Volume Distribution (VD):  0.445
Pgp-substrate:  1.6262859106063843%

ADMET: Metabolism

CYP1A2-inhibitor:  0.101
CYP1A2-substrate:  0.195
CYP2C19-inhibitor:  0.101
CYP2C19-substrate:  0.209
CYP2C9-inhibitor:  0.252
CYP2C9-substrate:  0.986
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.046
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.029

ADMET: Excretion

Clearance (CL):  3.862
Half-life (T1/2):  0.725

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.094
Drug-inuced Liver Injury (DILI):  0.041
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.679
Skin Sensitization:  0.895
Carcinogencity:  0.13
Eye Corrosion:  0.961
Eye Irritation:  0.987
Respiratory Toxicity:  0.831

Download Data

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

  Natural Product: NPC90904

Natural Product ID:  NPC90904
Common Name*:   3-Hydroxypalmitic Acid
IUPAC Name:   (3R)-3-hydroxyhexadecanoic acid
Synonyms:   3-Hydroxypalmitic Acid
Standard InCHIKey:  CBWALJHXHCJYTE-OAHLLOKOSA-N
Standard InCHI:  InChI=1S/C16H32O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-15(17)14-16(18)19/h15,17H,2-14H2,1H3,(H,18,19)/t15-/m1/s1
SMILES:  CCCCCCCCCCCCC[C@H](CC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2207728
PubChem CID:   15569776
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1078/0176-1617-00195]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[10757735]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[14735439]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. callus n.a. PMID[15715262]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[18220354]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[28445039]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota Roots n.a. n.a. PMID[30024167]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4391 Hypericum perforatum Species Hypericaceae 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
NPT20 Organism Candida albicans Candida albicans MIC = 12.5 ug.mL-1 PMID[522411]
NPT314 Organism Bacillus cereus Bacillus cereus MIC = 6.25 ug.mL-1 PMID[522411]

☑ 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 NPC90904 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
0.9565 High Similarity NPC131770
0.9565 High Similarity NPC200618
0.9348 High Similarity NPC328497
0.9348 High Similarity NPC324004
0.9149 High Similarity NPC106872
0.8723 High Similarity NPC12438
0.8723 High Similarity NPC30195
0.8571 High Similarity NPC304162
0.8511 High Similarity NPC469781
0.8462 Intermediate Similarity NPC469937
0.8462 Intermediate Similarity NPC320588
0.8462 Intermediate Similarity NPC53463
0.8462 Intermediate Similarity NPC23155
0.8298 Intermediate Similarity NPC76051
0.8298 Intermediate Similarity NPC74845
0.8261 Intermediate Similarity NPC307783
0.8261 Intermediate Similarity NPC196924
0.8261 Intermediate Similarity NPC209970
0.8261 Intermediate Similarity NPC216630
0.8261 Intermediate Similarity NPC149184
0.8261 Intermediate Similarity NPC171736
0.8125 Intermediate Similarity NPC287231
0.8125 Intermediate Similarity NPC47363
0.8085 Intermediate Similarity NPC67462
0.7885 Intermediate Similarity NPC100096
0.7843 Intermediate Similarity NPC26253
0.7826 Intermediate Similarity NPC261080
0.7826 Intermediate Similarity NPC14227
0.7826 Intermediate Similarity NPC279026
0.7826 Intermediate Similarity NPC301585
0.7826 Intermediate Similarity NPC113928
0.7826 Intermediate Similarity NPC154186
0.7826 Intermediate Similarity NPC301696
0.7826 Intermediate Similarity NPC201844
0.7797 Intermediate Similarity NPC314103
0.7755 Intermediate Similarity NPC8219
0.7719 Intermediate Similarity NPC17935
0.7719 Intermediate Similarity NPC470363
0.7708 Intermediate Similarity NPC203531
0.7708 Intermediate Similarity NPC236579
0.7692 Intermediate Similarity NPC55678
0.7667 Intermediate Similarity NPC476330
0.766 Intermediate Similarity NPC161097
0.766 Intermediate Similarity NPC28598
0.7627 Intermediate Similarity NPC474552
0.7551 Intermediate Similarity NPC255837
0.7551 Intermediate Similarity NPC19305
0.7451 Intermediate Similarity NPC21844
0.7447 Intermediate Similarity NPC118968
0.7447 Intermediate Similarity NPC294085
0.7447 Intermediate Similarity NPC183424
0.7447 Intermediate Similarity NPC214610
0.7419 Intermediate Similarity NPC469925
0.7414 Intermediate Similarity NPC475821
0.7347 Intermediate Similarity NPC301528
0.7347 Intermediate Similarity NPC71317
0.7347 Intermediate Similarity NPC129972
0.7308 Intermediate Similarity NPC477878
0.7308 Intermediate Similarity NPC324793
0.7292 Intermediate Similarity NPC149299
0.7292 Intermediate Similarity NPC40597
0.7292 Intermediate Similarity NPC165533
0.7292 Intermediate Similarity NPC256163
0.7292 Intermediate Similarity NPC250028
0.7292 Intermediate Similarity NPC12156
0.7288 Intermediate Similarity NPC243532
0.7255 Intermediate Similarity NPC52700
0.7255 Intermediate Similarity NPC145045
0.7255 Intermediate Similarity NPC105329
0.7255 Intermediate Similarity NPC63182
0.7234 Intermediate Similarity NPC54980
0.7234 Intermediate Similarity NPC22903
0.7234 Intermediate Similarity NPC305660
0.7234 Intermediate Similarity NPC268826
0.7234 Intermediate Similarity NPC201622
0.7222 Intermediate Similarity NPC287811
0.72 Intermediate Similarity NPC317128
0.7174 Intermediate Similarity NPC474392
0.7174 Intermediate Similarity NPC474914
0.7174 Intermediate Similarity NPC155263
0.7167 Intermediate Similarity NPC469923
0.7167 Intermediate Similarity NPC201939
0.7143 Intermediate Similarity NPC53541
0.7143 Intermediate Similarity NPC103286
0.7143 Intermediate Similarity NPC163746
0.7119 Intermediate Similarity NPC472020
0.7119 Intermediate Similarity NPC472019
0.7119 Intermediate Similarity NPC469924
0.7119 Intermediate Similarity NPC226602
0.7115 Intermediate Similarity NPC326957
0.7083 Intermediate Similarity NPC80234
0.7083 Intermediate Similarity NPC223249
0.7083 Intermediate Similarity NPC31551
0.7083 Intermediate Similarity NPC219536
0.7059 Intermediate Similarity NPC273545
0.7059 Intermediate Similarity NPC55023
0.7031 Intermediate Similarity NPC319007
0.7 Intermediate Similarity NPC472021
0.6957 Remote Similarity NPC168052
0.6957 Remote Similarity NPC250870
0.6957 Remote Similarity NPC191084
0.6957 Remote Similarity NPC156630
0.6957 Remote Similarity NPC317203
0.6957 Remote Similarity NPC97967
0.6923 Remote Similarity NPC314679
0.6875 Remote Similarity NPC104537
0.6875 Remote Similarity NPC127091
0.6875 Remote Similarity NPC206601
0.6875 Remote Similarity NPC22101
0.6875 Remote Similarity NPC330426
0.6875 Remote Similarity NPC148192
0.6875 Remote Similarity NPC271921
0.6842 Remote Similarity NPC289979
0.6825 Remote Similarity NPC245947
0.6825 Remote Similarity NPC136164
0.6825 Remote Similarity NPC255863
0.6818 Remote Similarity NPC42526
0.6809 Remote Similarity NPC134782
0.68 Remote Similarity NPC474361
0.6774 Remote Similarity NPC235788
0.6769 Remote Similarity NPC48218
0.6769 Remote Similarity NPC141481
0.6769 Remote Similarity NPC473559
0.6769 Remote Similarity NPC324981
0.6721 Remote Similarity NPC469921
0.6667 Remote Similarity NPC68343
0.6667 Remote Similarity NPC241265
0.6667 Remote Similarity NPC176500
0.6667 Remote Similarity NPC285003
0.6667 Remote Similarity NPC74352
0.6667 Remote Similarity NPC328089
0.6667 Remote Similarity NPC470320
0.6667 Remote Similarity NPC289686
0.6667 Remote Similarity NPC72722
0.6667 Remote Similarity NPC128996
0.6667 Remote Similarity NPC226592
0.6667 Remote Similarity NPC228411
0.6618 Remote Similarity NPC144419
0.6615 Remote Similarity NPC473829
0.6615 Remote Similarity NPC475443
0.6615 Remote Similarity NPC99619
0.6615 Remote Similarity NPC26500
0.6613 Remote Similarity NPC321838
0.661 Remote Similarity NPC477201
0.6607 Remote Similarity NPC470411
0.6607 Remote Similarity NPC470412
0.6607 Remote Similarity NPC314084
0.6607 Remote Similarity NPC470410
0.6571 Remote Similarity NPC474020
0.6567 Remote Similarity NPC470268
0.6567 Remote Similarity NPC321873
0.6567 Remote Similarity NPC476660
0.6562 Remote Similarity NPC318420
0.6562 Remote Similarity NPC215987
0.6562 Remote Similarity NPC322319
0.6562 Remote Similarity NPC469926
0.6562 Remote Similarity NPC326651
0.6562 Remote Similarity NPC325117
0.6562 Remote Similarity NPC306805
0.6562 Remote Similarity NPC326268
0.6552 Remote Similarity NPC261831
0.6552 Remote Similarity NPC6095
0.6552 Remote Similarity NPC290563
0.6552 Remote Similarity NPC88966
0.6552 Remote Similarity NPC281972
0.6552 Remote Similarity NPC424
0.6552 Remote Similarity NPC32467
0.6552 Remote Similarity NPC154245
0.6552 Remote Similarity NPC87394
0.6552 Remote Similarity NPC85813
0.6552 Remote Similarity NPC25417
0.6552 Remote Similarity NPC87564
0.6531 Remote Similarity NPC73245
0.6522 Remote Similarity NPC139131
0.6522 Remote Similarity NPC185538
0.6522 Remote Similarity NPC175342
0.6522 Remote Similarity NPC205141
0.6522 Remote Similarity NPC319034
0.6522 Remote Similarity NPC72324
0.6522 Remote Similarity NPC1748
0.6522 Remote Similarity NPC152759
0.6522 Remote Similarity NPC272998
0.6522 Remote Similarity NPC193062
0.6522 Remote Similarity NPC66124
0.6522 Remote Similarity NPC12231
0.6522 Remote Similarity NPC181516
0.6522 Remote Similarity NPC291158
0.6515 Remote Similarity NPC82315
0.6515 Remote Similarity NPC97736
0.6515 Remote Similarity NPC50228
0.6508 Remote Similarity NPC325773
0.6491 Remote Similarity NPC277878
0.6491 Remote Similarity NPC310746
0.6481 Remote Similarity NPC249754
0.6479 Remote Similarity NPC474003
0.6479 Remote Similarity NPC469867
0.6471 Remote Similarity NPC184550
0.6471 Remote Similarity NPC320119
0.6471 Remote Similarity NPC248763
0.6471 Remote Similarity NPC325452

  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 NPC90904 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
0.8462 Intermediate Similarity NPD3728 Approved
0.8462 Intermediate Similarity NPD3730 Approved
0.8261 Intermediate Similarity NPD2270 Approved
0.8125 Intermediate Similarity NPD2699 Approved
0.8113 Intermediate Similarity NPD3729 Clinical (unspecified phase)
0.7826 Intermediate Similarity NPD9448 Phase 2
0.7826 Intermediate Similarity NPD633 Phase 3
0.7755 Intermediate Similarity NPD3199 Clinical (unspecified phase)
0.7647 Intermediate Similarity NPD6125 Clinical (unspecified phase)
0.7609 Intermediate Similarity NPD3206 Approved
0.7447 Intermediate Similarity NPD9655 Approved
0.7414 Intermediate Similarity NPD3198 Approved
0.6935 Remote Similarity NPD7909 Approved
0.6935 Remote Similarity NPD3197 Phase 1
0.6923 Remote Similarity NPD634 Phase 3
0.6897 Remote Similarity NPD73 Approved
0.6786 Remote Similarity NPD3186 Phase 1
0.6607 Remote Similarity NPD9638 Phase 2
0.6552 Remote Similarity NPD4266 Approved
0.6552 Remote Similarity NPD3194 Approved
0.6552 Remote Similarity NPD3196 Approved
0.6552 Remote Similarity NPD3195 Phase 2
0.6522 Remote Similarity NPD5383 Approved
0.6522 Remote Similarity NPD2272 Approved
0.6491 Remote Similarity NPD9010 Approved
0.6491 Remote Similarity NPD66 Approved
0.6491 Remote Similarity NPD72 Approved
0.6491 Remote Similarity NPD65 Approved
0.6491 Remote Similarity NPD9011 Approved
0.6491 Remote Similarity NPD8960 Approved
0.6491 Remote Similarity NPD9007 Approved
0.6491 Remote Similarity NPD64 Approved
0.6491 Remote Similarity NPD9009 Approved
0.6491 Remote Similarity NPD9008 Approved
0.6379 Remote Similarity NPD3172 Approved
0.6364 Remote Similarity NPD2266 Phase 2
0.6364 Remote Similarity NPD622 Approved
0.6346 Remote Similarity NPD387 Clinical (unspecified phase)
0.6296 Remote Similarity NPD9431 Approved
0.6296 Remote Similarity NPD9430 Approved
0.6271 Remote Similarity NPD615 Clinical (unspecified phase)
0.619 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6164 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6164 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6094 Remote Similarity NPD4283 Discontinued
0.6078 Remote Similarity NPD77 Approved
0.6078 Remote Similarity NPD9450 Approved
0.6056 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6034 Remote Similarity NPD29 Approved
0.6034 Remote Similarity NPD28 Approved
0.6 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5968 Remote Similarity NPD8959 Approved
0.5965 Remote Similarity NPD8964 Approved
0.5946 Remote Similarity NPD4802 Phase 2
0.5946 Remote Similarity NPD3732 Approved
0.5946 Remote Similarity NPD4238 Approved
0.5942 Remote Similarity NPD8277 Approved
0.5921 Remote Similarity NPD5369 Approved
0.589 Remote Similarity NPD6117 Approved
0.5882 Remote Similarity NPD9513 Phase 1
0.5844 Remote Similarity NPD4270 Approved
0.5844 Remote Similarity NPD4269 Approved
0.5844 Remote Similarity NPD7345 Approved
0.5811 Remote Similarity NPD6116 Phase 1
0.5797 Remote Similarity NPD8278 Approved
0.5789 Remote Similarity NPD4252 Approved
0.5789 Remote Similarity NPD9005 Phase 3
0.5789 Remote Similarity NPD9004 Approved
0.5789 Remote Similarity NPD5368 Approved
0.5789 Remote Similarity NPD9003 Clinical (unspecified phase)
0.5763 Remote Similarity NPD9002 Approved
0.5763 Remote Similarity NPD9001 Clinical (unspecified phase)
0.5733 Remote Similarity NPD6114 Approved
0.5733 Remote Similarity NPD6697 Approved
0.5733 Remote Similarity NPD6115 Approved
0.5733 Remote Similarity NPD6118 Approved
0.5714 Remote Similarity NPD8857 Approved
0.569 Remote Similarity NPD3173 Approved
0.5686 Remote Similarity NPD9449 Clinical (unspecified phase)
0.5667 Remote Similarity NPD3215 Phase 1
0.566 Remote Similarity NPD7536 Approved
0.5652 Remote Similarity NPD896 Approved
0.5652 Remote Similarity NPD897 Approved
0.5652 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5652 Remote Similarity NPD898 Approved
0.5641 Remote Similarity NPD6435 Approved
0.5634 Remote Similarity NPD4244 Approved
0.5634 Remote Similarity NPD4245 Approved
0.5625 Remote Similarity NPD5363 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