Structure

Physi-Chem Properties

Molecular Weight:  334.07
Volume:  291.532
LogP:  3.754
LogD:  3.8
LogS:  -4.87
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.504
Synthetic Accessibility Score:  5.437
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.384
MDCK Permeability:  1.7324999134871177e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.715
Plasma Protein Binding (PPB):  95.7197494506836%
Volume Distribution (VD):  1.51
Pgp-substrate:  9.303110122680664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.831
CYP1A2-substrate:  0.705
CYP2C19-inhibitor:  0.93
CYP2C19-substrate:  0.924
CYP2C9-inhibitor:  0.847
CYP2C9-substrate:  0.544
CYP2D6-inhibitor:  0.089
CYP2D6-substrate:  0.371
CYP3A4-inhibitor:  0.877
CYP3A4-substrate:  0.895

ADMET: Excretion

Clearance (CL):  5.183
Half-life (T1/2):  0.233

ADMET: Toxicity

hERG Blockers:  0.093
Human Hepatotoxicity (H-HT):  0.283
Drug-inuced Liver Injury (DILI):  0.324
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.112
Maximum Recommended Daily Dose:  0.083
Skin Sensitization:  0.241
Carcinogencity:  0.242
Eye Corrosion:  0.963
Eye Irritation:  0.951
Respiratory Toxicity:  0.968

Download Data

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

  Natural Product: NPC30575

Natural Product ID:  NPC30575
Common Name*:   Pannosanol
IUPAC Name:   (2S,5R,6R,9R,10R)-10-bromo-9-chloro-2,5,9-trimethyl-1-methylidenespiro[5.5]undecan-5-ol
Synonyms:   Pannosanol
Standard InCHIKey:  VKWTTYZSKBUTGI-URWOTSEESA-N
Standard InCHI:  InChI=1S/C15H24BrClO/c1-10-5-6-14(4,18)15(11(10)2)8-7-13(3,17)12(16)9-15/h10,12,18H,2,5-9H2,1,3-4H3/t10-,12+,13+,14+,15+/m0/s1
SMILES:  C[C@H]1CC[C@](C)([C@@]2(CC[C@](C)([C@@H](C2)Br)Cl)C1=C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL450141
PubChem CID:   11142257
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

*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
NPO27012 Laurencia pannosa Species Rhodomelaceae Eukaryota n.a. Malaysian n.a. PMID[11374951]
NPO27012 Laurencia pannosa Species Rhodomelaceae 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
NPT2631 Organism Chromobacterium violaceum Chromobacterium violaceum MIC = 100.0 ug PMID[481303]
NPT172 Organism Proteus mirabilis Proteus mirabilis MIC = 60.0 ug PMID[481303]
NPT1549 Organism Vibrio cholerae Vibrio cholerae MIC = 100.0 ug PMID[481303]

☑ 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 NPC30575 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
0.8571 High Similarity NPC83436
0.7927 Intermediate Similarity NPC97491
0.7927 Intermediate Similarity NPC273356
0.7875 Intermediate Similarity NPC31330
0.7662 Intermediate Similarity NPC475077
0.7465 Intermediate Similarity NPC189290
0.7465 Intermediate Similarity NPC474769
0.7439 Intermediate Similarity NPC476603
0.7429 Intermediate Similarity NPC264779
0.7273 Intermediate Similarity NPC475786
0.7229 Intermediate Similarity NPC129501
0.7179 Intermediate Similarity NPC476604
0.716 Intermediate Similarity NPC474946
0.716 Intermediate Similarity NPC35397
0.7126 Intermediate Similarity NPC313115
0.7105 Intermediate Similarity NPC64123
0.7073 Intermediate Similarity NPC61080
0.7013 Intermediate Similarity NPC473929
0.6974 Remote Similarity NPC101128
0.6974 Remote Similarity NPC144650
0.6944 Remote Similarity NPC39068
0.6923 Remote Similarity NPC139207
0.6923 Remote Similarity NPC185874
0.6923 Remote Similarity NPC253303
0.6923 Remote Similarity NPC269077
0.6914 Remote Similarity NPC476609
0.6892 Remote Similarity NPC308569
0.6892 Remote Similarity NPC469582
0.6892 Remote Similarity NPC469572
0.6889 Remote Similarity NPC188896
0.6889 Remote Similarity NPC76909
0.6883 Remote Similarity NPC258595
0.6883 Remote Similarity NPC282619
0.6883 Remote Similarity NPC208198
0.6883 Remote Similarity NPC11555
0.6883 Remote Similarity NPC172613
0.6883 Remote Similarity NPC2728
0.6883 Remote Similarity NPC60837
0.6835 Remote Similarity NPC276616
0.6835 Remote Similarity NPC94192
0.6835 Remote Similarity NPC244790
0.6824 Remote Similarity NPC476610
0.6818 Remote Similarity NPC282598
0.6753 Remote Similarity NPC68656
0.675 Remote Similarity NPC476431
0.6747 Remote Similarity NPC476605
0.6744 Remote Similarity NPC113024
0.6711 Remote Similarity NPC282694
0.6711 Remote Similarity NPC79576
0.6711 Remote Similarity NPC110214
0.6711 Remote Similarity NPC41160
0.6711 Remote Similarity NPC194208
0.6707 Remote Similarity NPC95165
0.6706 Remote Similarity NPC215307
0.6706 Remote Similarity NPC274750
0.6667 Remote Similarity NPC476606
0.6667 Remote Similarity NPC311891
0.6667 Remote Similarity NPC476607
0.6632 Remote Similarity NPC299714
0.6632 Remote Similarity NPC257510
0.663 Remote Similarity NPC224552
0.663 Remote Similarity NPC239453
0.6625 Remote Similarity NPC245795
0.6593 Remote Similarity NPC174273
0.6588 Remote Similarity NPC476608
0.6585 Remote Similarity NPC167706
0.6582 Remote Similarity NPC475897
0.6582 Remote Similarity NPC103734
0.6522 Remote Similarity NPC131453
0.6506 Remote Similarity NPC83368
0.65 Remote Similarity NPC88454
0.65 Remote Similarity NPC117607
0.65 Remote Similarity NPC101307
0.6486 Remote Similarity NPC179024
0.6463 Remote Similarity NPC283316
0.6463 Remote Similarity NPC163020
0.6463 Remote Similarity NPC92801
0.6463 Remote Similarity NPC45296
0.6452 Remote Similarity NPC329643
0.6429 Remote Similarity NPC475793
0.6429 Remote Similarity NPC476366
0.6429 Remote Similarity NPC201048
0.6429 Remote Similarity NPC237510
0.6429 Remote Similarity NPC22134
0.642 Remote Similarity NPC208999
0.642 Remote Similarity NPC2648
0.6386 Remote Similarity NPC301226
0.6386 Remote Similarity NPC164022
0.6386 Remote Similarity NPC111234
0.6375 Remote Similarity NPC476406
0.6375 Remote Similarity NPC279434
0.6353 Remote Similarity NPC3403
0.6341 Remote Similarity NPC210323
0.6341 Remote Similarity NPC9942
0.631 Remote Similarity NPC182717
0.631 Remote Similarity NPC211009
0.631 Remote Similarity NPC471799
0.6286 Remote Similarity NPC100445
0.6279 Remote Similarity NPC106364
0.6279 Remote Similarity NPC265588
0.6279 Remote Similarity NPC470766
0.6279 Remote Similarity NPC300324
0.6279 Remote Similarity NPC470749
0.6279 Remote Similarity NPC63958
0.6279 Remote Similarity NPC91573
0.6279 Remote Similarity NPC240604
0.6265 Remote Similarity NPC475728
0.625 Remote Similarity NPC476737
0.625 Remote Similarity NPC291379
0.625 Remote Similarity NPC27243
0.625 Remote Similarity NPC474768
0.6237 Remote Similarity NPC280810
0.6235 Remote Similarity NPC49168
0.6235 Remote Similarity NPC100334
0.6235 Remote Similarity NPC192638
0.6235 Remote Similarity NPC471797
0.6235 Remote Similarity NPC196358
0.6235 Remote Similarity NPC5046
0.6235 Remote Similarity NPC477138
0.6235 Remote Similarity NPC145552
0.6235 Remote Similarity NPC243342
0.6235 Remote Similarity NPC25511
0.6235 Remote Similarity NPC62657
0.6235 Remote Similarity NPC476736
0.6235 Remote Similarity NPC254509
0.6235 Remote Similarity NPC472503
0.6235 Remote Similarity NPC308440
0.6224 Remote Similarity NPC156912
0.6222 Remote Similarity NPC215175
0.622 Remote Similarity NPC139785
0.622 Remote Similarity NPC266578
0.6207 Remote Similarity NPC198968
0.6207 Remote Similarity NPC471798
0.6207 Remote Similarity NPC155986
0.6207 Remote Similarity NPC470758
0.6207 Remote Similarity NPC318495
0.6207 Remote Similarity NPC470711
0.6203 Remote Similarity NPC174956
0.6203 Remote Similarity NPC81615
0.619 Remote Similarity NPC242992
0.618 Remote Similarity NPC15714
0.6163 Remote Similarity NPC230301
0.6163 Remote Similarity NPC70982
0.6163 Remote Similarity NPC22105
0.6163 Remote Similarity NPC134847
0.6163 Remote Similarity NPC136188
0.6163 Remote Similarity NPC230704
0.6163 Remote Similarity NPC476424
0.6163 Remote Similarity NPC104387
0.6163 Remote Similarity NPC231256
0.6163 Remote Similarity NPC144075
0.6163 Remote Similarity NPC212879
0.6163 Remote Similarity NPC285893
0.6163 Remote Similarity NPC291503
0.6163 Remote Similarity NPC32832
0.6163 Remote Similarity NPC200243
0.6163 Remote Similarity NPC162742
0.6163 Remote Similarity NPC39362
0.6163 Remote Similarity NPC304309
0.6163 Remote Similarity NPC66566
0.6163 Remote Similarity NPC178383
0.6163 Remote Similarity NPC477923
0.6163 Remote Similarity NPC185536
0.6163 Remote Similarity NPC288035
0.6163 Remote Similarity NPC240235
0.6163 Remote Similarity NPC28657
0.6162 Remote Similarity NPC92231
0.6162 Remote Similarity NPC34732
0.6154 Remote Similarity NPC135648
0.6145 Remote Similarity NPC234511
0.6143 Remote Similarity NPC14552
0.6136 Remote Similarity NPC42853
0.6136 Remote Similarity NPC301707
0.6136 Remote Similarity NPC31828
0.6136 Remote Similarity NPC285761
0.6136 Remote Similarity NPC472501
0.6136 Remote Similarity NPC472342
0.6136 Remote Similarity NPC474989
0.6136 Remote Similarity NPC22955
0.6136 Remote Similarity NPC470396
0.6136 Remote Similarity NPC99168
0.6133 Remote Similarity NPC67508
0.6133 Remote Similarity NPC84824
0.6129 Remote Similarity NPC76164
0.6129 Remote Similarity NPC153699
0.6125 Remote Similarity NPC219940
0.6118 Remote Similarity NPC265485
0.6118 Remote Similarity NPC220939
0.6118 Remote Similarity NPC195489
0.6098 Remote Similarity NPC197805
0.6098 Remote Similarity NPC263161
0.6092 Remote Similarity NPC278091
0.6092 Remote Similarity NPC96319
0.6092 Remote Similarity NPC237460
0.6092 Remote Similarity NPC290598
0.6092 Remote Similarity NPC27765
0.6092 Remote Similarity NPC113733
0.6092 Remote Similarity NPC265328
0.6092 Remote Similarity NPC78067
0.6092 Remote Similarity NPC86305

  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 NPC30575 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
0.6235 Remote Similarity NPD4784 Approved
0.6235 Remote Similarity NPD4785 Approved
0.619 Remote Similarity NPD4243 Approved
0.6163 Remote Similarity NPD6942 Approved
0.6163 Remote Similarity NPD7339 Approved
0.6092 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6 Remote Similarity NPD7525 Registered
0.5977 Remote Similarity NPD4190 Phase 3
0.5977 Remote Similarity NPD5275 Approved
0.5889 Remote Similarity NPD7645 Phase 2
0.5862 Remote Similarity NPD6924 Approved
0.5862 Remote Similarity NPD6926 Approved
0.573 Remote Similarity NPD6933 Approved
0.5714 Remote Similarity NPD4195 Approved
0.5699 Remote Similarity NPD3667 Approved
0.5632 Remote Similarity NPD7150 Approved
0.5632 Remote Similarity NPD7152 Approved
0.5632 Remote Similarity NPD7151 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