Structure

Physi-Chem Properties

Molecular Weight:  381.22
Volume:  382.199
LogP:  1.639
LogD:  2.029
LogS:  -1.933
# Rotatable Bonds:  16
TPSA:  130.08
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.183
Synthetic Accessibility Score:  3.783
Fsp3:  0.882
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.5
MDCK Permeability:  6.502363248728216e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.939
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.166
Plasma Protein Binding (PPB):  96.12183380126953%
Volume Distribution (VD):  0.633
Pgp-substrate:  1.9954910278320312%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.073
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.165
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.857
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.231
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.018

ADMET: Excretion

Clearance (CL):  2.67
Half-life (T1/2):  0.465

ADMET: Toxicity

hERG Blockers:  0.138
Human Hepatotoxicity (H-HT):  0.658
Drug-inuced Liver Injury (DILI):  0.021
AMES Toxicity:  0.061
Rat Oral Acute Toxicity:  0.405
Maximum Recommended Daily Dose:  0.313
Skin Sensitization:  0.953
Carcinogencity:  0.38
Eye Corrosion:  0.968
Eye Irritation:  0.694
Respiratory Toxicity:  0.982

Download Data

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

  Natural Product: NPC212008

Natural Product ID:  NPC212008
Common Name*:   KZLMQHDECHRBBR-DIKSDDLMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KZLMQHDECHRBBR-DIKSDDLMSA-N
Standard InCHI:  InChI=1S/C17H35NO6S/c1-2-3-4-5-6-7-8-9-10-11-12-13-16(24-25(21,22)23)17(20)15(18)14-19/h11-12,15-17,19-20H,2-10,13-14,18H2,1H3,(H,21,22,23)/b12-11+/t15-,16+,17-/m0/s1
SMILES:  CCCCCCCCCC/C=C/C[C@H]([C@H]([C@H](CO)N)O)OS(=O)(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL484668
PubChem CID:   10091252
10959895
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000403] Organic sulfuric acids and derivatives
        • [CHEMONTID:0003455] Sulfuric acid esters
          • [CHEMONTID:0001185] Sulfuric acid monoesters

*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
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[10579872]
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[11325244]
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[12088447]
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[22182501]

☑ 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
NPT81 Cell Line A549 Homo sapiens ED50 = 0.3 ug ml-1 PMID[452446]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 0.3 ug ml-1 PMID[452446]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 0.3 ug ml-1 PMID[452446]
NPT574 Cell Line XF498 Homo sapiens ED50 = 0.3 ug ml-1 PMID[452446]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 0.3 ug ml-1 PMID[452446]

☑ 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 NPC212008 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 NPC140327
1.0 High Similarity NPC51055
1.0 High Similarity NPC62293
0.9324 High Similarity NPC207657
0.831 Intermediate Similarity NPC113224
0.8158 Intermediate Similarity NPC3094
0.8 Intermediate Similarity NPC47333
0.7692 Intermediate Similarity NPC264417
0.7692 Intermediate Similarity NPC217095
0.7654 Intermediate Similarity NPC79367
0.7639 Intermediate Similarity NPC55068
0.7429 Intermediate Similarity NPC168308
0.7429 Intermediate Similarity NPC302569
0.7286 Intermediate Similarity NPC8979
0.7179 Intermediate Similarity NPC324638
0.7093 Intermediate Similarity NPC477199
0.6988 Remote Similarity NPC475363
0.6988 Remote Similarity NPC473971
0.6988 Remote Similarity NPC473972
0.6932 Remote Similarity NPC258824
0.6914 Remote Similarity NPC288086
0.6905 Remote Similarity NPC314762
0.6786 Remote Similarity NPC474833
0.6714 Remote Similarity NPC123814
0.6625 Remote Similarity NPC291196
0.6625 Remote Similarity NPC103712
0.6585 Remote Similarity NPC314678
0.6585 Remote Similarity NPC26932
0.6579 Remote Similarity NPC17455
0.6506 Remote Similarity NPC473588
0.6506 Remote Similarity NPC78562
0.6479 Remote Similarity NPC474322
0.6404 Remote Similarity NPC228638
0.6386 Remote Similarity NPC305223
0.6383 Remote Similarity NPC61894
0.6383 Remote Similarity NPC475603
0.6344 Remote Similarity NPC39290
0.6344 Remote Similarity NPC159369
0.6341 Remote Similarity NPC474674
0.6341 Remote Similarity NPC476694
0.6341 Remote Similarity NPC476696
0.6341 Remote Similarity NPC476695
0.6316 Remote Similarity NPC329003
0.6316 Remote Similarity NPC326524
0.6316 Remote Similarity NPC325550
0.6316 Remote Similarity NPC319131
0.622 Remote Similarity NPC475930
0.622 Remote Similarity NPC127145
0.622 Remote Similarity NPC137620
0.622 Remote Similarity NPC474675
0.6184 Remote Similarity NPC321030
0.6154 Remote Similarity NPC145627
0.6154 Remote Similarity NPC321838
0.6143 Remote Similarity NPC29222
0.6143 Remote Similarity NPC96966
0.6143 Remote Similarity NPC121062
0.6111 Remote Similarity NPC474312
0.6105 Remote Similarity NPC319021
0.6098 Remote Similarity NPC23721
0.6098 Remote Similarity NPC268922
0.6071 Remote Similarity NPC474468
0.6053 Remote Similarity NPC52012
0.6042 Remote Similarity NPC182632
0.6042 Remote Similarity NPC282705
0.6024 Remote Similarity NPC473710
0.6024 Remote Similarity NPC475694
0.6 Remote Similarity NPC281590
0.6 Remote Similarity NPC315170
0.6 Remote Similarity NPC82799
0.6 Remote Similarity NPC242930
0.598 Remote Similarity NPC477198
0.5976 Remote Similarity NPC471418
0.5938 Remote Similarity NPC242503
0.5938 Remote Similarity NPC74672
0.5938 Remote Similarity NPC139782
0.5938 Remote Similarity NPC209047
0.5938 Remote Similarity NPC43074
0.593 Remote Similarity NPC470993
0.593 Remote Similarity NPC470992
0.5918 Remote Similarity NPC262312
0.5918 Remote Similarity NPC35269
0.5918 Remote Similarity NPC70323
0.5918 Remote Similarity NPC23454
0.5905 Remote Similarity NPC315531
0.5904 Remote Similarity NPC474812
0.589 Remote Similarity NPC261571
0.5876 Remote Similarity NPC473950
0.5876 Remote Similarity NPC15851
0.5876 Remote Similarity NPC111567
0.5876 Remote Similarity NPC263545
0.5876 Remote Similarity NPC473581
0.5876 Remote Similarity NPC309898
0.5876 Remote Similarity NPC473604
0.5876 Remote Similarity NPC186840
0.5876 Remote Similarity NPC475125
0.5875 Remote Similarity NPC477106
0.5862 Remote Similarity NPC476924
0.5857 Remote Similarity NPC76976
0.5854 Remote Similarity NPC83965
0.5854 Remote Similarity NPC315141
0.5854 Remote Similarity NPC129995
0.5844 Remote Similarity NPC323436
0.5814 Remote Similarity NPC470435
0.5811 Remote Similarity NPC49494
0.5811 Remote Similarity NPC188341
0.5802 Remote Similarity NPC474928
0.58 Remote Similarity NPC45313
0.5783 Remote Similarity NPC22101
0.5783 Remote Similarity NPC470663
0.5783 Remote Similarity NPC104537
0.5783 Remote Similarity NPC127091
0.5783 Remote Similarity NPC330426
0.5783 Remote Similarity NPC271921
0.5783 Remote Similarity NPC26500
0.5783 Remote Similarity NPC99619
0.5783 Remote Similarity NPC148192
0.5783 Remote Similarity NPC195165
0.578 Remote Similarity NPC314306
0.5765 Remote Similarity NPC97614
0.5758 Remote Similarity NPC256570
0.5758 Remote Similarity NPC282088
0.5758 Remote Similarity NPC157353
0.5758 Remote Similarity NPC17290
0.5758 Remote Similarity NPC158445
0.5758 Remote Similarity NPC192066
0.5758 Remote Similarity NPC156782
0.5758 Remote Similarity NPC3568
0.5758 Remote Similarity NPC54961
0.575 Remote Similarity NPC29468
0.5741 Remote Similarity NPC477997
0.5733 Remote Similarity NPC477724
0.5733 Remote Similarity NPC26102
0.5733 Remote Similarity NPC187361
0.5733 Remote Similarity NPC270041
0.5733 Remote Similarity NPC474496
0.5732 Remote Similarity NPC476655
0.5732 Remote Similarity NPC286851
0.5732 Remote Similarity NPC303798
0.5732 Remote Similarity NPC476654
0.5732 Remote Similarity NPC477525
0.5732 Remote Similarity NPC476657
0.5729 Remote Similarity NPC316186
0.5714 Remote Similarity NPC324981
0.5714 Remote Similarity NPC74035
0.5714 Remote Similarity NPC473559
0.5714 Remote Similarity NPC141481
0.5714 Remote Similarity NPC48218
0.57 Remote Similarity NPC470382
0.57 Remote Similarity NPC119225
0.57 Remote Similarity NPC471635
0.57 Remote Similarity NPC476261
0.57 Remote Similarity NPC25033
0.5699 Remote Similarity NPC196102
0.5699 Remote Similarity NPC178758
0.5686 Remote Similarity NPC132931
0.5684 Remote Similarity NPC477389
0.5684 Remote Similarity NPC477387
0.5676 Remote Similarity NPC473672
0.5676 Remote Similarity NPC474495
0.5676 Remote Similarity NPC200772
0.5673 Remote Similarity NPC325339
0.5673 Remote Similarity NPC72401
0.5663 Remote Similarity NPC60424
0.5663 Remote Similarity NPC476656
0.5663 Remote Similarity NPC314221
0.5663 Remote Similarity NPC476659
0.566 Remote Similarity NPC475918
0.5658 Remote Similarity NPC49059
0.5658 Remote Similarity NPC256209
0.5644 Remote Similarity NPC8098
0.5644 Remote Similarity NPC197294
0.5644 Remote Similarity NPC183449
0.5641 Remote Similarity NPC470970
0.5632 Remote Similarity NPC55652
0.5625 Remote Similarity NPC81896
0.5625 Remote Similarity NPC57846
0.5625 Remote Similarity NPC30126
0.5625 Remote Similarity NPC321919
0.5625 Remote Similarity NPC130807
0.5625 Remote Similarity NPC243532
0.5625 Remote Similarity NPC62507
0.5625 Remote Similarity NPC8087
0.5625 Remote Similarity NPC474014
0.5619 Remote Similarity NPC55336
0.5614 Remote Similarity NPC477515
0.5614 Remote Similarity NPC313802
0.5614 Remote Similarity NPC314268
0.5614 Remote Similarity NPC67917
0.561 Remote Similarity NPC223386
0.561 Remote Similarity NPC471780
0.561 Remote Similarity NPC476658
0.561 Remote Similarity NPC142290
0.561 Remote Similarity NPC475221
0.561 Remote Similarity NPC471892
0.561 Remote Similarity NPC75435
0.561 Remote Similarity NPC253468
0.561 Remote Similarity NPC235311
0.561 Remote Similarity NPC198341
0.5607 Remote Similarity NPC319537
0.5607 Remote Similarity NPC313272

  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 NPC212008 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
0.7639 Intermediate Similarity NPD3210 Clinical (unspecified phase)
0.7179 Intermediate Similarity NPD3212 Clinical (unspecified phase)
0.6714 Remote Similarity NPD3215 Phase 1
0.6429 Remote Similarity NPD3214 Discontinued
0.6023 Remote Similarity NPD3732 Approved
0.5938 Remote Similarity NPD8522 Clinical (unspecified phase)
0.578 Remote Similarity NPD6429 Approved
0.578 Remote Similarity NPD6430 Approved
0.575 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5696 Remote Similarity NPD9240 Approved
0.5696 Remote Similarity NPD9239 Approved
0.5632 Remote Similarity NPD9034 Approved
0.5632 Remote Similarity NPD67 Phase 2
0.561 Remote Similarity NPD3197 Phase 1

  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