Structure of PDB 1rbm Chain A Binding Site BS01

Receptor Information
>1rbm Chain A (length=200) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAG
IPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKW
NGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIIL
QEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV
Ligand information
Ligand IDKT5
InChIInChI=1S/C42H54F3N9O20/c43-42(44,45)41(73,74)21(3-1-2-20-32(46)53-40(47)54-34(20)62)18-4-6-19(7-5-18)33(61)52-26(39(71)72)11-16-30(58)50-24(37(67)68)9-14-28(56)48-22(35(63)64)8-13-27(55)49-23(36(65)66)10-15-29(57)51-25(38(69)70)12-17-31(59)60/h4-7,21-26,73-74H,1-3,8-17H2,(H,48,56)(H,49,55)(H,50,58)(H,51,57)(H,52,61)(H,59,60)(H,63,64)(H,65,66)(H,67,68)(H,69,70)(H,71,72)(H5,46,47,53,54,62)/t21-,22?,23?,24?,25?,26-/m0/s1
InChIKeyIWEGOVKIJZGOSL-RCZRCYCLSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)c1ccc(cc1)C(C(O)(O)C(F)(F)F)CCCc2c(O)nc(nc2N)N)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1C(CCCc2c(nc(nc2O)N)N)C(C(F)(F)F)(O)O)C(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O
CACTVS 3.341Nc1nc(N)c(CCC[CH](c2ccc(cc2)C(=O)N[CH](CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)(O)C(F)(F)F)c(O)n1
CACTVS 3.341Nc1nc(N)c(CCC[C@@H](c2ccc(cc2)C(=O)N[C@@H](CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)(O)C(F)(F)F)c(O)n1
OpenEye OEToolkits 1.5.0c1cc(ccc1[C@H](CCCc2c(nc(nc2O)N)N)C(C(F)(F)F)(O)O)C(=O)N[C@@H](CCC(=O)N[C@H](CCC(=O)N[C@H](CCC(=O)N[C@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O
FormulaC42 H54 F3 N9 O20
NameN-{4-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDRO-PYRIMIDIN-5-YL)-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXY-ETHYL)-BUT-2-YL-BENZOYL}-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GLUTAMIC ACID
ChEMBL
DrugBank
ZINC
PDB chain1rbm Chain A Residue 510 [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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PDB1rbm Human GAR Tfase complex structure
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R64 M89 R90 I91 L92 N106 H108 G117 S118 V139 A140 E141 V143 D144
Binding residue
(residue number reindexed from 1)		R64 M89 R90 I91 L92 N106 H108 G117 S118 V139 A140 E141 V143 D144
Annotation score1
Binding affinityMOAD: Ki=4nM
Enzymatic activity
Catalytic site (original residue number in PDB) N106 H108 T135 D144
Catalytic site (residue number reindexed from 1) N106 H108 T135 D144
Enzyme Commision number 2.1.2.2: phosphoribosylglycinamide formyltransferase 1.
6.3.3.1: phosphoribosylformylglycinamidine cyclo-ligase.
6.3.4.13: phosphoribosylamine--glycine ligase.
Gene Ontology
Molecular Function
GO:0004644 phosphoribosylglycinamide formyltransferase activity
Biological Process
GO:0006189 'de novo' IMP biosynthetic process
GO:0009058 biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1rbm, PDBe:1rbm, PDBj:1rbm
PDBsum1rbm
PubMed
UniProtP22102|PUR2_HUMAN Trifunctional purine biosynthetic protein adenosine-3 (Gene Name=GART)

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