Structure of PDB 3pz2 Chain B Binding Site BS03

Receptor Information
>3pz2 Chain B (length=322) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKDVTIKSDAPDTLLLEKHADYIASYGSEYCMSEYLRMSGVYWGLTVMDL
MGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLYD
SIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKL
DAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQ
VNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWID
REKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKPV
SPVFCMPEEVLQRVNVQPELVS
Ligand information
Ligand ID3PZ
InChIInChI=1S/C29H29N5O3S/c1-32-21-31-17-26(32)20-33-19-25(15-22-6-4-3-5-7-22)34(18-24-14-23(16-30)8-13-29(24)33)38(35,36)28-11-9-27(37-2)10-12-28/h3-14,17,21,25H,15,18-20H2,1-2H3/t25-/m1/s1
InChIKeyBJWZXDNEKWSGQH-RUZDIDTESA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=S(=O)(c1ccc(OC)cc1)N3C(CN(c2c(cc(C#N)cc2)C3)Cc4cncn4C)Cc5ccccc5
CACTVS 3.370COc1ccc(cc1)[S](=O)(=O)N2Cc3cc(ccc3N(C[CH]2Cc4ccccc4)Cc5cncn5C)C#N
CACTVS 3.370COc1ccc(cc1)[S](=O)(=O)N2Cc3cc(ccc3N(C[C@H]2Cc4ccccc4)Cc5cncn5C)C#N
OpenEye OEToolkits 1.7.0Cn1cncc1CN2C[C@H]([N@@](Cc3c2ccc(c3)C#N)S(=O)(=O)c4ccc(cc4)OC)Cc5ccccc5
OpenEye OEToolkits 1.7.0Cn1cncc1CN2CC(N(Cc3c2ccc(c3)C#N)S(=O)(=O)c4ccc(cc4)OC)Cc5ccccc5
FormulaC29 H29 N5 O3 S
Name(3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile
ChEMBLCHEMBL1738728
DrugBank
ZINCZINC000032303467
PDB chain3pz2 Chain B Residue 333 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3pz2 Structure-Guided Development of Selective RabGGTase Inhibitors.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		Y44 D238 W244 D287 F289 H290
Binding residue
(residue number reindexed from 1)		Y35 D229 W235 D278 F280 H281
Annotation score1
Binding affinityMOAD: ic50=724nM
PDBbind-CN: -logKd/Ki=6.14,IC50=724nM
Enzymatic activity
Catalytic site (original residue number in PDB) H190 R232 K235 D238 C240 Y241 D280 D287 H290
Catalytic site (residue number reindexed from 1) H181 R223 K226 D229 C231 Y232 D271 D278 H281
Enzyme Commision number 2.5.1.60: protein geranylgeranyltransferase type II.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004659 prenyltransferase activity
GO:0004661 protein geranylgeranyltransferase activity
GO:0004663 Rab geranylgeranyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008318 protein prenyltransferase activity
GO:0019840 isoprenoid binding
GO:0031267 small GTPase binding
GO:0046872 metal ion binding
Biological Process
GO:0018344 protein geranylgeranylation
Cellular Component
GO:0005968 Rab-protein geranylgeranyltransferase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3pz2, PDBe:3pz2, PDBj:3pz2
PDBsum3pz2
PubMed21520375
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

[Back to BioLiP]