NPASS Compound

Structure

NPC473646 OpenBabel07101719142D 65 66 0 0 1 0 0 0 0 0999 V2000 -11.0672 14.5132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.7990 14.5391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4758 0.8981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7680 3.4626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2686 10.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2536 11.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4101 9.4878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.1120 11.5135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4251 8.4880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0971 12.5134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5666 7.9751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.9555 13.0263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5816 6.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3461 -3.3608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4126 -4.3207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2119 -4.3517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5833 -4.4103 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4689 -2.2516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7257 -2.9207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3985 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1627 3.9237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7221 0.6643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9604 -0.8418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.9406 14.0262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4608 1.8980 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8946 3.9496 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5550 -2.7491 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8330 -3.4133 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4204 -0.9074 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7439 0.8722 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.9754 -1.8417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2866 -4.7310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0037 -5.3177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0676 -1.4426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7231 6.4623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3043 3.4108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8796 4.9495 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5874 2.3850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8111 -3.6213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4054 -1.9072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7724 0.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0062 5.4365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1523 -5.7219 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.4281 -6.1354 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.0622 -1.3381 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.8597 -2.4207 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.1478 4.9236 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.3193 2.4109 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.7826 -3.3842 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0419 -2.8016 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7289 1.8721 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.7381 5.4624 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.0362 3.4367 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9535 -2.0496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4955 -4.1192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9997 -5.4073 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8497 6.9493 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4309 3.8978 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5724 3.3849 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8261 -4.6211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3769 -2.1443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3251 1.5295 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9913 6.4364 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5131 0.0526 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 24 1 0 0 0 0 2 24 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 6 8 1 0 0 0 0 7 9 1 0 0 0 0 8 10 1 0 0 0 0 9 11 1 0 0 0 0 10 12 1 0 0 0 0 11 13 1 0 0 0 0 12 24 1 0 0 0 0 13 35 1 0 0 0 0 14 16 1 0 0 0 0 15 17 1 0 0 0 0 16 32 1 0 0 0 0 17 33 1 0 0 0 0 18 19 2 0 0 0 0 18 45 1 0 0 0 0 19 46 1 0 0 0 0 20 34 1 0 0 0 0 21 36 1 0 0 0 0 21 47 1 0 0 0 0 22 30 1 0 0 0 0 22 65 1 0 0 0 0 23 31 1 0 0 0 0 23 65 1 0 0 0 0 25 3 1 6 0 0 0 25 38 1 0 0 0 0 25 48 1 0 0 0 0 26 4 1 6 0 0 0 26 37 1 0 0 0 0 26 54 1 0 0 0 0 27 14 1 1 0 0 0 27 31 1 0 0 0 0 27 49 1 0 0 0 0 28 15 1 1 0 0 0 28 39 1 0 0 0 0 28 50 1 0 0 0 0 29 20 1 1 0 0 0 29 40 1 0 0 0 0 29 51 1 0 0 0 0 30 41 1 0 0 0 0 30 52 1 6 0 0 0 31 55 2 0 0 0 0 32 43 2 0 0 0 0 32 56 1 0 0 0 0 33 44 2 0 0 0 0 33 57 1 0 0 0 0 34 45 2 0 0 0 0 34 46 1 0 0 0 0 35 53 2 3 0 0 0 35 58 1 0 0 0 0 36 48 2 3 0 0 0 36 59 1 0 0 0 0 37 42 1 6 0 0 0 37 53 1 0 0 0 0 38 52 2 3 0 0 0 38 60 1 0 0 0 0 39 49 2 3 0 0 0 39 61 1 0 0 0 0 40 50 2 3 0 0 0 40 62 1 0 0 0 0 41 51 2 3 0 0 0 41 63 1 0 0 0 0 42 47 2 3 0 0 0 42 64 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	919.51
Volume:	912.685
LogP:	-0.453
LogD:	0.569
LogS:	-1.785
# Rotatable Bonds:	29
TPSA:	381.03
# H-Bond Aceptor:	23
# H-Bond Donor:	13
# Rings:	2
# Heavy Atoms:	23

MedChem Properties

QED Drug-Likeness Score:	0.036
Synthetic Accessibility Score:	6.411
Fsp3:	0.69
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:	-3.55
MDCK Permeability:	0.00031043728813529015
Pgp-inhibitor:	0.791
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.995
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.839
Plasma Protein Binding (PPB):	32.62709426879883%
Volume Distribution (VD):	0.399
Pgp-substrate:	51.355098724365234%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.002
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.021
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.033
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.023
CYP3A4-inhibitor:	0.039
CYP3A4-substrate:	0.0

ADMET: Excretion

Clearance (CL):	1.623
Half-life (T1/2):	0.747

ADMET: Toxicity

hERG Blockers:	0.0
Human Hepatotoxicity (H-HT):	1.0
Drug-inuced Liver Injury (DILI):	0.965
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.013
Skin Sensitization:	0.86
Carcinogencity:	0.41
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.98

Download Data

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

Natural Product: NPC473646

Natural Product ID:	NPC473646
*Common Name:**	11-Methyl-Dodecanoic Acid {(1S,2R)-1-[({(S)-1-[(3S,6S,9S,12S)-9,12-Bis-(2-Carbamoyl-Ethyl)-6-(1H-Imidazol-2-Ylmethyl)-4,7,10,13-Tetraoxo-1-Oxa-5,8,11-Triaza-Cyclotetradec-3-Ylcarbamoyl]-Ethylcarbamoyl}-Methyl)-Carbamoyl]-2-Hydroxy-Propyl}-Amide
IUPAC Name:	N-[(2S,3R)-1-[[2-[[(2S)-1-[[(3S,6S,9S,12S)-9,12-bis(3-amino-3-oxopropyl)-6-(1H-imidazol-2-ylmethyl)-4,7,10,13-tetraoxo-1-oxa-5,8,11-triazacyclotetradec-3-yl]amino]-1-oxopropan-2-yl]amino]-2-oxoethyl]amino]-3-hydroxy-1-oxobutan-2-yl]-11-methyldodecanamide
Synonyms:
Standard InCHIKey:	XFMZOMIXLZCGAO-VUICESKMSA-N
Standard InCHI:	InChI=1S/C42H69N11O12/c1-24(2)12-10-8-6-5-7-9-11-13-35(58)53-37(26(4)54)42(64)47-21-36(59)48-25(3)38(60)52-30-22-65-23-31(55)27(14-16-32(43)56)49-39(61)28(15-17-33(44)57)50-40(62)29(51-41(30)63)20-34-45-18-19-46-34/h18-19,24-30,37,54H,5-17,20-23H2,1-4H3,(H2,43,56)(H2,44,57)(H,45,46)(H,47,64)(H,48,59)(H,49,61)(H,50,62)(H,51,63)(H,52,60)(H,53,58)/t25-,26+,27-,28-,29-,30-,37-/m0/s1
SMILES:	CC(C)CCCCCCCCCC(=O)NC(C(C)O)C(=O)NCC(=O)NC(C)C(=O)NC1COCC(=O)C(NC(=O)C(NC(=O)C(NC1=O)CC2=NC=CN2)CCC(=O)N)CCC(=O)N
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL448094
PubChem CID:	44558933
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0002010] Hybrid peptides

*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
NPO19369	Bacillus thuringiensis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11087590]
NPO19369	Bacillus thuringiensis	Species	Bacillaceae	Bacteria	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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3483	Organism	Stachybotrys chartarum	Stachybotrys chartarum	IZ	=	10.0	mm	PMID[543162]

☑ 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 NPC473646 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	226
0.1-0.2	8775
0.2-0.3	26783
0.3-0.4	5366
0.4-0.5	1367
0.5-0.6	162
0.6-0.7	17
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.6978	Remote Similarity	NPC313504
0.6573	Remote Similarity	NPC313897
0.6225	Remote Similarity	NPC238945
0.6182	Remote Similarity	NPC185903
0.6182	Remote Similarity	NPC286696
0.6131	Remote Similarity	NPC174020
0.6092	Remote Similarity	NPC60537
0.6	Remote Similarity	NPC18223
0.6	Remote Similarity	NPC327477
0.6	Remote Similarity	NPC237812
0.5969	Remote Similarity	NPC313514
0.5938	Remote Similarity	NPC180462
0.5928	Remote Similarity	NPC210947
0.5864	Remote Similarity	NPC477118
0.5833	Remote Similarity	NPC477120
0.5815	Remote Similarity	NPC290959
0.5812	Remote Similarity	NPC24589
0.5803	Remote Similarity	NPC282458
0.5803	Remote Similarity	NPC78941
0.5798	Remote Similarity	NPC477119
0.5793	Remote Similarity	NPC25465
0.5793	Remote Similarity	NPC235501
0.5779	Remote Similarity	NPC327613
0.5765	Remote Similarity	NPC201900
0.574	Remote Similarity	NPC470139
0.5714	Remote Similarity	NPC15566
0.5689	Remote Similarity	NPC126634
0.5655	Remote Similarity	NPC470140

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 NPC473646 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	118
0.1-0.2	1016
0.2-0.3	3970
0.3-0.4	2955
0.4-0.5	938
0.5-0.6	142
0.6-0.7	11
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6886	Remote Similarity	NPD3697	Discontinued
0.6687	Remote Similarity	NPD7842	Phase 2
0.6554	Remote Similarity	NPD3105	Discontinued
0.6402	Remote Similarity	NPD1451	Approved
0.6386	Remote Similarity	NPD8271	Discontinued
0.6265	Remote Similarity	NPD5342	Clinical (unspecified phase)
0.625	Remote Similarity	NPD5768	Phase 2
0.6242	Remote Similarity	NPD300	Approved
0.6159	Remote Similarity	NPD1808	Phase 1
0.6158	Remote Similarity	NPD3130	Discontinued
0.6114	Remote Similarity	NPD8641	Approved
0.6092	Remote Similarity	NPD2180	Approved
0.6048	Remote Similarity	NPD1431	Approved
0.6048	Remote Similarity	NPD1430	Approved
0.6023	Remote Similarity	NPD2604	Approved
0.602	Remote Similarity	NPD8410	Clinical (unspecified phase)
0.6012	Remote Similarity	NPD9183	Clinical (unspecified phase)
0.6	Remote Similarity	NPD9133	Approved
0.6	Remote Similarity	NPD8119	Discontinued
0.6	Remote Similarity	NPD9628	Approved
0.5988	Remote Similarity	NPD875	Clinical (unspecified phase)
0.5974	Remote Similarity	NPD1368	Approved
0.5969	Remote Similarity	NPD7138	Phase 2
0.5943	Remote Similarity	NPD1731	Clinical (unspecified phase)
0.5933	Remote Similarity	NPD8105	Discontinued
0.5931	Remote Similarity	NPD7465	Suspended
0.593	Remote Similarity	NPD8629	Discontinued
0.5915	Remote Similarity	NPD8075	Discontinued
0.5882	Remote Similarity	NPD3706	Clinical (unspecified phase)
0.5872	Remote Similarity	NPD7531	Clinical (unspecified phase)
0.5855	Remote Similarity	NPD9412	Discontinued
0.5854	Remote Similarity	NPD8261	Discontinued
0.5843	Remote Similarity	NPD1120	Approved
0.5843	Remote Similarity	NPD1121	Approved
0.5833	Remote Similarity	NPD5683	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD7981	Discontinued
0.5833	Remote Similarity	NPD5684	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD5682	Phase 3
0.5784	Remote Similarity	NPD7834	Approved
0.5756	Remote Similarity	NPD9627	Approved
0.5724	Remote Similarity	NPD613	Phase 2
0.5682	Remote Similarity	NPD3708	Phase 2
0.5679	Remote Similarity	NPD4812	Phase 1
0.5667	Remote Similarity	NPD2646	Discontinued
0.5635	Remote Similarity	NPD8030	Approved
0.5629	Remote Similarity	NPD9196	Phase 2
0.5629	Remote Similarity	NPD9345	Clinical (unspecified phase)
0.5628	Remote Similarity	NPD8113	Phase 2
0.5618	Remote Similarity	NPD536	Clinical (unspecified phase)
0.5613	Remote Similarity	NPD7980	Clinical (unspecified phase)
0.561	Remote Similarity	NPD1356	Approved
0.561	Remote Similarity	NPD1355	Clinical (unspecified phase)
0.561	Remote Similarity	NPD1354	Approved
0.5608	Remote Similarity	NPD3108	Clinical (unspecified phase)
0.5607	Remote Similarity	NPD566	Approved
0.5607	Remote Similarity	NPD568	Approved
0.5607	Remote Similarity	NPD567	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