NPASS Compound

Natural Product: NPC153400

Natural Product ID	NPC153400
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Gastrin
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL413654
PubChem CID	44288444
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0003297] Organic Polymers [CHEMONTID:0003298] Polypeptides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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46 1 0 46 47 2 3 47 48 1 0 48 49 1 0 48 50 1 0 50 51 2 3 51 52 1 0 52 53 1 0 53 54 1 0 54 55 2 0 55 56 1 0 56 57 2 0 57 58 1 0 58 59 2 0 57 60 1 0 52 61 1 0 61 62 2 3 62 63 1 0 63 64 1 0 64 65 2 3 65 66 1 0 66 67 1 0 67 68 1 0 68 69 2 0 69 70 1 0 70 71 1 0 71 72 2 0 72 73 1 0 73 74 2 0 74 75 1 0 75 76 2 0 66 77 1 0 77 78 2 3 78 79 1 0 79 80 1 0 80 81 1 0 81 82 1 0 82 83 1 0 79 84 1 0 84 85 2 3 85 86 1 0 86 87 1 0 87 88 1 0 88 89 2 0 88 90 1 0 86 91 1 0 91 92 2 3 92 93 1 0 93 94 1 0 94 95 1 0 95 96 2 0 96 97 1 0 97 98 2 0 98 99 1 0 99100 2 0 93101 1 0 101102 2 3 101103 1 0 91104 1 0 84105 1 0 77106 1 0 64107 1 0 61108 1 0 50109 1 0 46110 1 0 38111 1 0 30112 1 0 22113 1 0 14114 1 0 6115 1 0 5116 1 0 116117 2 3 117118 1 0 118119 1 0 119120 1 0 120121 2 0 121122 1 0 122123 1 0 123124 2 0 124125 1 0 125126 2 0 126127 1 0 127128 2 0 118129 1 0 129130 2 3 130131 1 0 131132 1 0 132133 1 0 133134 1 0 134135 1 0 135136 1 0 136137 2 0 136138 1 0 138139 1 0 139140 2 3 140141 1 0 141142 1 0 142143 1 0 143144 1 0 144145 2 0 144146 1 0 141147 1 0 140148 1 0 130149 1 0 117150 1 0 59 54 1 0 76 68 1 0 100 95 1 0 128120 1 0 135131 1 0 76 71 1 0 128123 1 0 1151 1 0 1152 1 0 1153 1 0 2154 1 0 3155 1 0 3156 1 0 3157 1 0 4158 1 0 4159 1 0 5160 1 6 8161 1 1 9162 1 0 9163 1 0 10164 1 0 10165 1 0 13166 1 0 16167 1 6 17168 1 0 17169 1 0 18170 1 0 18171 1 0 21172 1 0 24173 1 6 25174 1 0 25175 1 0 26176 1 0 26177 1 0 29178 1 0 32179 1 1 33180 1 0 33181 1 0 34182 1 0 34183 1 0 37184 1 0 40185 1 6 41186 1 0 41187 1 0 42188 1 0 42189 1 0 45190 1 0 48191 1 1 49192 1 0 49193 1 0 49194 1 0 52195 1 6 53196 1 0 53197 1 0 55198 1 0 56199 1 0 58200 1 0 59201 1 0 60202 1 0 63203 1 0 63204 1 0 66205 1 1 67206 1 0 67207 1 0 69208 1 0 70209 1 0 72210 1 0 73211 1 0 74212 1 0 75213 1 0 79214 1 6 80215 1 0 80216 1 0 81217 1 0 81218 1 0 83219 1 0 83220 1 0 83221 1 0 86222 1 6 87223 1 0 87224 1 0 90225 1 0 93226 1 1 94227 1 0 94228 1 0 96229 1 0 97230 1 0 98231 1 0 99232 1 0 100233 1 0 102234 1 0 103235 1 0 104236 1 0 105237 1 0 106238 1 0 107239 1 0 108240 1 0 109241 1 0 110242 1 0 111243 1 0 112244 1 0 113245 1 0 114246 1 0 115247 1 0 118248 1 1 119249 1 0 119250 1 0 121251 1 0 122252 1 0 124253 1 0 125254 1 0 126255 1 0 127256 1 0 131257 1 6 132258 1 0 132259 1 0 133260 1 0 133261 1 0 134262 1 0 134263 1 0 138264 1 0 138265 1 0 141266 1 1 142267 1 0 142268 1 0 143269 1 0 143270 1 0 146271 1 0 147272 1 0 147273 1 0 148274 1 0 149275 1 0 150276 1 0 M END

Standard InCHIKey	AOXOCDRNSPFDPE-UKEONUMOSA-N
Standard InCHI	InChI=1S/C97H126N20O32S/c1-49(2)39-68(114-95(147)71(43-54-46-101-60-18-11-9-16-57(54)60)116-97(149)73-19-12-37-117(73)75(120)48-103-85(137)58(98)24-30-76(121)122)93(145)110-65(29-35-81(131)132)91(143)109-64(28-34-80(129)130)90(142)108-63(27-33-79(127)128)89(141)107-62(26-32-78(125)126)88(140)106-61(25-31-77(123)124)87(139)104-50(3)84(136)113-69(41-52-20-22-55(118)23-21-52)86(138)102-47-74(119)105-70(42-53-45-100-59-17-10-8-15-56(53)59)94(146)111-66(36-38-150-4)92(144)115-72(44-82(133)134)96(148)112-67(83(99)135)40-51-13-6-5-7-14-51/h5-11,13-18,20-23,45-46,49-50,58,61-73,100-101,118H,12,19,24-44,47-48,98H2,1-4H3,(H2,99,135)(H,102,138)(H,103,137)(H,104,139)(H,105,119)(H,106,140)(H,107,141)(H,108,142)(H,109,143)(H,110,145)(H,111,146)(H,112,148)(H,113,136)(H,114,147)(H,115,144)(H,116,149)(H,121,122)(H,123,124)(H,125,126)(H,127,128)(H,129,130)(H,131,132)(H,133,134)/t50-,58+,61-,62-,63-,64+,65+,66-,67-,68+,69-,70-,71+,72-,73+/m1/s1
SMILES	CC(C)C[C@@H](C(=N[C@@H](CCC(=O)O)C(=N[C@@H](CCC(=O)O)C(=N[C@H](CCC(=O)O)C(=N[C@H](CCC(=O)O)C(=N[C@H](CCC(=O)O)C(=N[C@H](C)C(=N[C@H](Cc1ccc(cc1)O)C(=NCC(=N[C@H](Cc1c[nH]c2ccccc12)C(=N[C@H](CCSC)C(=N[C@H](CC(=O)O)C(=N[C@H](Cc1ccccc1)C(=N)O)O)O)O)O)O)O)O)O)O)O)O)O)N=C([C@H](Cc1c[nH]c2ccccc12)N=C([C@@H]1CCCN1C(=O)CN=C([C@H](CCC(=O)O)N)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	2114.86	Volume:	2045.918 ? Van der Waals volume.
Dense:	1.034	LogP:	0.384 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.56 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.8 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	66.0	Rigid Bonds:	61.0
TPSA:	892.17 ? Topological Polar Surface Area.	H-Bond Acceptor:	52.0
H-Bond Donor:	29.0	Rings:	7.0
Heavy Atoms:	53.0

MedChem Properties

QED Drug-Likeness Score:	0.012	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	8.407	Fsp³:	0.464
MCE-18:	217.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.663	Fluc inhibitor:	0.18 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.261 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.668 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.766	Promiscuous compounds:	0.031

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.432	MDCK Permeability:	-5.215
Pgp-inhibitor:	0.0	Pgp-substrate:	0.985
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.999
20% Bioavailability (F20%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.003
Plasma Protein Binding (PPB):	50.386%	Volume Distribution (VD):	-0.614
Fu:	47.682% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.013

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.0 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

-1.622

Half-life (T1/2):

6.634

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	1.0	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	0.105	Rat Oral Acute Toxicity:	0.516
Maximum Recommended Daily Dose:	0.949	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.587
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.998
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	0.0	Hek293 Cytotoxicity:	0.002
BCF:	-0.478 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	2.491 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.123 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.664 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	PMID[27439360]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27364	Gallus gallus	Species	Phasianidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27364	Gallus gallus	Species	Phasianidae	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	Organism Name	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
Kd	2
EC50	2
IC50	1

Activity Type	# Activity
Individual protein	4
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT4730	Individual protein	Cholecystokinin B receptor	Rattus norvegicus	Kd	=	1.4	nM	PMID[7966139]
NPT4730	Individual protein	Cholecystokinin B receptor	Rattus norvegicus	EC50	=	1000.0	nM	PMID[7966139]
NPT4729	Individual protein	Cholecystokinin B receptor	Homo sapiens	Kd	=	3.2	nM	PMID[7966139]
NPT4731	Individual protein	Cholecystokinin A receptor	Rattus norvegicus	IC50	=	0.2	nM	PMID[6094810]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	n.a.	EC50	=	600.0	nM	PMID[7966139]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC153400 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	24983
0.1-0.2	23492
0.2-0.3	1042
0.3-0.4	225
0.4-0.5	91
0.5-0.6	25
0.6-0.7	0
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	Natural Product ID
0.5811	Remote Similarity	NPC483985
0.5706	Remote Similarity	NPC479141
0.5695	Remote Similarity	NPC489555
0.5464	Remote Similarity	NPC486515
0.5455	Remote Similarity	NPC479075
0.5435	Remote Similarity	NPC483341
0.5379	Remote Similarity	NPC479065
0.5368	Remote Similarity	NPC477634
0.5342	Remote Similarity	NPC479073
0.527	Remote Similarity	NPC479066
0.5257	Remote Similarity	NPC486513
0.5241	Remote Similarity	NPC155143
0.5226	Remote Similarity	NPC325976
0.5226	Remote Similarity	NPC326363
0.5187	Remote Similarity	NPC484965
0.5156	Remote Similarity	NPC477633
0.5134	Remote Similarity	NPC477635
0.5104	Remote Similarity	NPC479128
0.5101	Remote Similarity	NPC479076
0.5097	Remote Similarity	NPC479872
0.5079	Remote Similarity	NPC486506
0.5079	Remote Similarity	NPC485247
0.5079	Remote Similarity	NPC486514
0.5034	Remote Similarity	NPC162860
0.5033	Remote Similarity	NPC75726

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC153400 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3591
0.1-0.2	5305
0.2-0.3	217
0.3-0.4	25
0.4-0.5	10
0.5-0.6	2
0.6-0.7	0
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
0.5342	Remote Similarity	NPD8073	Phase 4
0.5338	Remote Similarity	NPD8072	Approved

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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