Structure of PDB 6z48 Chain D Binding Site BS03

Receptor Information
>6z48 Chain D (length=254) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETVGK
GQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGD
SGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVI
DQFG
Ligand information
Ligand IDX1V
InChIInChI=1S/C26H32ClN5O5S3/c1-15(2)22-26(37)29-13-16-4-3-5-17(12-16)23(34)31-18(14-30-25(36)19-6-7-20(27)40-19)24(35)28-9-11-39-38-10-8-21(33)32-22/h3-7,12,15,18,22H,8-11,13-14H2,1-2H3,(H,28,35)(H,29,37)(H,30,36)(H,31,34)(H,32,33)/t18-,22+/m0/s1
InChIKeyYNRUDSNJNOWNHB-PGRDOPGGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)[C@@H]1C(=O)NCc2cccc(c2)C(=O)N[C@H](C(=O)NCCSSCCC(=O)N1)CNC(=O)c3ccc(s3)Cl
CACTVS 3.385CC(C)[C@H]1NC(=O)CCSSCCNC(=O)[C@H](CNC(=O)c2sc(Cl)cc2)NC(=O)c3cccc(CNC1=O)c3
OpenEye OEToolkits 2.0.7CC(C)C1C(=O)NCc2cccc(c2)C(=O)NC(C(=O)NCCSSCCC(=O)N1)CNC(=O)c3ccc(s3)Cl
CACTVS 3.385CC(C)[CH]1NC(=O)CCSSCCNC(=O)[CH](CNC(=O)c2sc(Cl)cc2)NC(=O)c3cccc(CNC1=O)c3
FormulaC26 H32 Cl N5 O5 S3
Name5-chloranyl-N-[[(4S,15R)-2,5,13,16-tetrakis(oxidanylidene)-15-propan-2-yl-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide;
macrocycle X1vE;
5-chloro-N-[[(4S,15R)-15-isopropyl-2,5,13,16-tetraoxo-9,10-dithia-3,6,14,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23),20-trien-4-yl]methyl]thiophene-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6z48 Chain D Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6z48 Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale.
Resolution2.27 Å
Binding residue
(original residue number in PDB)
H57 Y60A W60D N98 L99 I174 D189 A190 C191 E192 V213 S214 W215 G216 E217 G219 G226 F227 Y228
Binding residue
(residue number reindexed from 1)
H43 Y47 W50 N95 L96 I175 D195 A196 C197 E198 V221 S222 W223 G224 E225 G226 G234 F235 Y236
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

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Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6z48, PDBe:6z48, PDBj:6z48
PDBsum6z48
PubMed35780129
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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