Structure

Physi-Chem Properties

Molecular Weight:  204.14
Volume:  208.121
LogP:  -0.692
LogD:  -0.798
LogS:  0.289
# Rotatable Bonds:  4
TPSA:  80.92
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.498
Synthetic Accessibility Score:  4.198
Fsp3:  1.0
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:  -5.257
MDCK Permeability:  0.001080449903383851
Pgp-inhibitor:  0.006
Pgp-substrate:  0.311
Human Intestinal Absorption (HIA):  0.557
20% Bioavailability (F20%):  0.921
30% Bioavailability (F30%):  0.933

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.15
Plasma Protein Binding (PPB):  12.932024002075195%
Volume Distribution (VD):  0.747
Pgp-substrate:  81.80677032470703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.096
CYP2C19-inhibitor:  0.007
CYP2C19-substrate:  0.191
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.035
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.082
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.097

ADMET: Excretion

Clearance (CL):  4.461
Half-life (T1/2):  0.892

ADMET: Toxicity

hERG Blockers:  0.041
Human Hepatotoxicity (H-HT):  0.683
Drug-inuced Liver Injury (DILI):  0.034
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.753
Skin Sensitization:  0.88
Carcinogencity:  0.907
Eye Corrosion:  0.279
Eye Irritation:  0.982
Respiratory Toxicity:  0.793

Download Data

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

  Natural Product: NPC307022

Natural Product ID:  NPC307022
Common Name*:   (1S,2R,5S)-2-(2-Hydroxyethyl)-2,5-Bis(Hydroxymethyl)Cyclohexan-1-Ol
IUPAC Name:   (1S,2R,5S)-2-(2-hydroxyethyl)-2,5-bis(hydroxymethyl)cyclohexan-1-ol
Synonyms:  
Standard InCHIKey:  GTYDEUZIKIEUMD-LPEHRKFASA-N
Standard InCHI:  InChI=1S/C10H20O4/c11-4-3-10(7-13)2-1-8(6-12)5-9(10)14/h8-9,11-14H,1-7H2/t8-,9-,10+/m0/s1
SMILES:  C1C[C@@](CCO)(CO)[C@H](C[C@H]1CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3262207
PubChem CID:   90676290
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols
            • [CHEMONTID:0002647] Cyclohexanols

*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
NPO9348 Cananga odorata Species Annonaceae Eukaryota fruits n.a. n.a. PMID[11374955]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[21504145]
NPO9348 Cananga odorata Species Annonaceae Eukaryota flower buds Thailand n.a. PMID[24601675]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9348 Cananga odorata Species Annonaceae 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 = 45.0 % PMID[465796]
NPT2 Others Unspecified Inhibition = 55.1 % PMID[465796]
NPT2 Others Unspecified Inhibition = 55.9 % PMID[465796]
NPT2 Others Unspecified Inhibition = 51.6 % PMID[465796]
NPT2 Others Unspecified Inhibition = 25.6 % PMID[465796]
NPT27 Others Unspecified Activity > 95.2 % PMID[465796]
NPT2 Others Unspecified IC50 = 2000.0 nM PMID[465796]

☑ 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 NPC307022 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
0.8367 Intermediate Similarity NPC176309
0.8367 Intermediate Similarity NPC198540
0.8367 Intermediate Similarity NPC147343
0.8367 Intermediate Similarity NPC84030
0.8367 Intermediate Similarity NPC287550
0.8367 Intermediate Similarity NPC223468
0.8148 Intermediate Similarity NPC471269
0.7963 Intermediate Similarity NPC53209
0.7857 Intermediate Similarity NPC236588
0.7719 Intermediate Similarity NPC215671
0.7719 Intermediate Similarity NPC87296
0.7719 Intermediate Similarity NPC475515
0.7627 Intermediate Similarity NPC185547
0.7627 Intermediate Similarity NPC95804
0.76 Intermediate Similarity NPC240994
0.7544 Intermediate Similarity NPC135438
0.7414 Intermediate Similarity NPC47663
0.74 Intermediate Similarity NPC144891
0.7344 Intermediate Similarity NPC470833
0.7288 Intermediate Similarity NPC185116
0.7258 Intermediate Similarity NPC472946
0.7258 Intermediate Similarity NPC172613
0.7258 Intermediate Similarity NPC60837
0.7258 Intermediate Similarity NPC2728
0.7258 Intermediate Similarity NPC208198
0.7258 Intermediate Similarity NPC11555
0.7258 Intermediate Similarity NPC282619
0.7231 Intermediate Similarity NPC471879
0.7193 Intermediate Similarity NPC67508
0.7193 Intermediate Similarity NPC84824
0.7193 Intermediate Similarity NPC89069
0.7193 Intermediate Similarity NPC166894
0.7193 Intermediate Similarity NPC178223
0.7193 Intermediate Similarity NPC277917
0.7193 Intermediate Similarity NPC283655
0.717 Intermediate Similarity NPC314087
0.7143 Intermediate Similarity NPC102336
0.7143 Intermediate Similarity NPC161473
0.7143 Intermediate Similarity NPC44122
0.7143 Intermediate Similarity NPC160261
0.7143 Intermediate Similarity NPC36002
0.7143 Intermediate Similarity NPC469759
0.7097 Intermediate Similarity NPC94897
0.7097 Intermediate Similarity NPC101128
0.7077 Intermediate Similarity NPC66407
0.7077 Intermediate Similarity NPC107919
0.7031 Intermediate Similarity NPC473230
0.7031 Intermediate Similarity NPC139207
0.7031 Intermediate Similarity NPC475884
0.7031 Intermediate Similarity NPC185874
0.7031 Intermediate Similarity NPC476928
0.6984 Remote Similarity NPC260116
0.6984 Remote Similarity NPC80463
0.697 Remote Similarity NPC251201
0.697 Remote Similarity NPC232925
0.697 Remote Similarity NPC63588
0.6964 Remote Similarity NPC476149
0.6964 Remote Similarity NPC244869
0.6964 Remote Similarity NPC476136
0.6964 Remote Similarity NPC300235
0.6949 Remote Similarity NPC150713
0.6949 Remote Similarity NPC29976
0.6935 Remote Similarity NPC209686
0.6935 Remote Similarity NPC114891
0.6935 Remote Similarity NPC249078
0.6935 Remote Similarity NPC292419
0.6935 Remote Similarity NPC236099
0.6935 Remote Similarity NPC290791
0.6923 Remote Similarity NPC469987
0.6923 Remote Similarity NPC472741
0.6923 Remote Similarity NPC474756
0.6912 Remote Similarity NPC475458
0.6912 Remote Similarity NPC470151
0.6912 Remote Similarity NPC304499
0.6875 Remote Similarity NPC142712
0.6875 Remote Similarity NPC177022
0.6866 Remote Similarity NPC478103
0.6866 Remote Similarity NPC100586
0.6866 Remote Similarity NPC109457
0.6866 Remote Similarity NPC157422
0.6866 Remote Similarity NPC1340
0.6866 Remote Similarity NPC470071
0.6866 Remote Similarity NPC187471
0.6866 Remote Similarity NPC127094
0.6866 Remote Similarity NPC252182
0.6825 Remote Similarity NPC144650
0.6825 Remote Similarity NPC118937
0.6825 Remote Similarity NPC167995
0.6825 Remote Similarity NPC281540
0.6825 Remote Similarity NPC159654
0.6825 Remote Similarity NPC219940
0.6818 Remote Similarity NPC99264
0.6818 Remote Similarity NPC477820
0.6812 Remote Similarity NPC243027
0.6812 Remote Similarity NPC139765
0.6812 Remote Similarity NPC196136
0.6812 Remote Similarity NPC131584
0.6812 Remote Similarity NPC317242
0.6812 Remote Similarity NPC472952
0.6812 Remote Similarity NPC472950
0.6812 Remote Similarity NPC158208
0.6792 Remote Similarity NPC108441
0.6792 Remote Similarity NPC77550
0.6786 Remote Similarity NPC274261
0.6786 Remote Similarity NPC291724
0.6774 Remote Similarity NPC71460
0.6774 Remote Similarity NPC218585
0.6774 Remote Similarity NPC148174
0.6769 Remote Similarity NPC204233
0.6769 Remote Similarity NPC179823
0.6769 Remote Similarity NPC269077
0.6769 Remote Similarity NPC253303
0.6769 Remote Similarity NPC48079
0.6765 Remote Similarity NPC470610
0.6765 Remote Similarity NPC253805
0.6727 Remote Similarity NPC294858
0.6719 Remote Similarity NPC474380
0.6719 Remote Similarity NPC300442
0.6719 Remote Similarity NPC473276
0.6719 Remote Similarity NPC41577
0.6719 Remote Similarity NPC258595
0.6716 Remote Similarity NPC283316
0.6716 Remote Similarity NPC92801
0.6716 Remote Similarity NPC192192
0.6716 Remote Similarity NPC282454
0.6714 Remote Similarity NPC163597
0.6667 Remote Similarity NPC276616
0.6667 Remote Similarity NPC291147
0.6667 Remote Similarity NPC10476
0.6667 Remote Similarity NPC61665
0.6667 Remote Similarity NPC48795
0.6667 Remote Similarity NPC192501
0.6667 Remote Similarity NPC228994
0.6667 Remote Similarity NPC119425
0.6667 Remote Similarity NPC244790
0.6667 Remote Similarity NPC478130
0.6667 Remote Similarity NPC475893
0.6667 Remote Similarity NPC14552
0.662 Remote Similarity NPC128951
0.662 Remote Similarity NPC302578
0.662 Remote Similarity NPC477227
0.662 Remote Similarity NPC307865
0.662 Remote Similarity NPC185915
0.662 Remote Similarity NPC192046
0.662 Remote Similarity NPC105208
0.6618 Remote Similarity NPC157777
0.6618 Remote Similarity NPC164022
0.6618 Remote Similarity NPC131506
0.6615 Remote Similarity NPC473929
0.6613 Remote Similarity NPC204173
0.6613 Remote Similarity NPC475412
0.661 Remote Similarity NPC300189
0.6604 Remote Similarity NPC313795
0.66 Remote Similarity NPC221022
0.6567 Remote Similarity NPC254037
0.6567 Remote Similarity NPC241085
0.6567 Remote Similarity NPC210323
0.6567 Remote Similarity NPC299948
0.6567 Remote Similarity NPC470830
0.6567 Remote Similarity NPC129829
0.6567 Remote Similarity NPC234511
0.6562 Remote Similarity NPC69149
0.6562 Remote Similarity NPC68656
0.6562 Remote Similarity NPC225415
0.6557 Remote Similarity NPC182903
0.6557 Remote Similarity NPC476735
0.6528 Remote Similarity NPC177343
0.6528 Remote Similarity NPC18857
0.6528 Remote Similarity NPC147993
0.6528 Remote Similarity NPC67657
0.6522 Remote Similarity NPC153719
0.6522 Remote Similarity NPC95165
0.6515 Remote Similarity NPC472984
0.6515 Remote Similarity NPC63190
0.65 Remote Similarity NPC3025
0.65 Remote Similarity NPC170780
0.6481 Remote Similarity NPC473914
0.6479 Remote Similarity NPC63958
0.6471 Remote Similarity NPC231945
0.6462 Remote Similarity NPC476330
0.6441 Remote Similarity NPC32222
0.6441 Remote Similarity NPC202146
0.6438 Remote Similarity NPC477282
0.6438 Remote Similarity NPC81074
0.6438 Remote Similarity NPC287452
0.6438 Remote Similarity NPC269333
0.6429 Remote Similarity NPC475793
0.6429 Remote Similarity NPC472944
0.6429 Remote Similarity NPC166250
0.6429 Remote Similarity NPC237510
0.6429 Remote Similarity NPC472945
0.6429 Remote Similarity NPC308489
0.6418 Remote Similarity NPC2648
0.6418 Remote Similarity NPC471238
0.6418 Remote Similarity NPC266578
0.6418 Remote Similarity NPC245795
0.6406 Remote Similarity NPC83200
0.6393 Remote Similarity NPC322148
0.6389 Remote Similarity NPC11907
0.6389 Remote Similarity NPC207010

  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 NPC307022 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
0.8367 Intermediate Similarity NPD384 Approved
0.8367 Intermediate Similarity NPD385 Approved
0.7097 Intermediate Similarity NPD371 Approved
0.7077 Intermediate Similarity NPD4267 Clinical (unspecified phase)
0.6792 Remote Similarity NPD388 Approved
0.6792 Remote Similarity NPD386 Approved
0.6538 Remote Similarity NPD1462 Approved
0.6471 Remote Similarity NPD1460 Approved
0.6389 Remote Similarity NPD6116 Phase 1
0.6324 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6324 Remote Similarity NPD3700 Clinical (unspecified phase)
0.625 Remote Similarity NPD6117 Approved
0.6232 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6232 Remote Similarity NPD4787 Phase 1
0.6212 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6167 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6143 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6143 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6133 Remote Similarity NPD7525 Registered
0.6111 Remote Similarity NPD3703 Phase 2
0.6087 Remote Similarity NPD3698 Phase 2
0.6081 Remote Similarity NPD6114 Approved
0.6081 Remote Similarity NPD6118 Approved
0.6081 Remote Similarity NPD6697 Approved
0.6081 Remote Similarity NPD6115 Approved
0.6038 Remote Similarity NPD9426 Discontinued
0.6 Remote Similarity NPD7645 Phase 2
0.6 Remote Similarity NPD4244 Approved
0.6 Remote Similarity NPD4245 Approved
0.5972 Remote Similarity NPD1811 Approved
0.5972 Remote Similarity NPD1810 Approved
0.5972 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5902 Remote Similarity NPD615 Clinical (unspecified phase)
0.5775 Remote Similarity NPD4789 Approved
0.5758 Remote Similarity NPD368 Approved
0.5714 Remote Similarity NPD6705 Phase 1
0.5714 Remote Similarity NPD6928 Phase 2
0.5694 Remote Similarity NPD3187 Discontinued
0.5658 Remote Similarity NPD3671 Phase 1
0.56 Remote Similarity NPD3701 Clinical (unspecified phase)

  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