Structure of PDB 1a4r Chain A Binding Site BS01
Receptor Information
>1a4r Chain A (length=190) Species:
9606
(Homo sapiens) [
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MQTIKCVVVGDVAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEP
YTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPE
ITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLK
AVKYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVL
Ligand information
Ligand ID
GDP
InChI
InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKey
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.7.6
c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385
NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385
NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01
O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Formula
C10 H15 N5 O11 P2
Name
GUANOSINE-5'-DIPHOSPHATE
ChEMBL
CHEMBL384759
DrugBank
DB04315
ZINC
ZINC000008215481
PDB chain
1a4r Chain A Residue 200 [
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Receptor-Ligand Complex Structure
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PDB
1a4r
Nucleotide binding to the G12V-mutant of Cdc42 investigated by X-ray diffraction and fluorescence spectroscopy: two different nucleotide states in one crystal.
Resolution
2.5 Å
Binding residue
(original residue number in PDB)
A13 V14 G15 K16 T17 C18 F28 Q116 D118 L119 S158 A159 L160
Binding residue
(residue number reindexed from 1)
A13 V14 G15 K16 T17 C18 F28 Q116 D118 L119 S158 A159 L160
Annotation score
4
Binding affinity
MOAD
: Kd=9.4pM
Enzymatic activity
Enzyme Commision number
3.6.5.2
: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924
GTPase activity
GO:0003925
G protein activity
GO:0005515
protein binding
GO:0005525
GTP binding
GO:0016787
hydrolase activity
GO:0019901
protein kinase binding
GO:0030742
GTP-dependent protein binding
GO:0031435
mitogen-activated protein kinase kinase kinase binding
GO:0031996
thioesterase binding
GO:0032427
GBD domain binding
GO:0034191
apolipoprotein A-I receptor binding
GO:0042802
identical protein binding
GO:0061630
ubiquitin protein ligase activity
Biological Process
GO:0002040
sprouting angiogenesis
GO:0003015
heart process
GO:0003161
cardiac conduction system development
GO:0003253
cardiac neural crest cell migration involved in outflow tract morphogenesis
GO:0006897
endocytosis
GO:0006911
phagocytosis, engulfment
GO:0007015
actin filament organization
GO:0007030
Golgi organization
GO:0007088
regulation of mitotic nuclear division
GO:0007097
nuclear migration
GO:0007163
establishment or maintenance of cell polarity
GO:0007229
integrin-mediated signaling pathway
GO:0007264
small GTPase-mediated signal transduction
GO:0007399
nervous system development
GO:0008104
protein localization
GO:0009653
anatomical structure morphogenesis
GO:0010591
regulation of lamellipodium assembly
GO:0010592
positive regulation of lamellipodium assembly
GO:0021762
substantia nigra development
GO:0030036
actin cytoskeleton organization
GO:0030154
cell differentiation
GO:0030225
macrophage differentiation
GO:0030307
positive regulation of cell growth
GO:0030335
positive regulation of cell migration
GO:0031274
positive regulation of pseudopodium assembly
GO:0031333
negative regulation of protein-containing complex assembly
GO:0032467
positive regulation of cytokinesis
GO:0032488
Cdc42 protein signal transduction
GO:0032956
regulation of actin cytoskeleton organization
GO:0034329
cell junction assembly
GO:0034332
adherens junction organization
GO:0035050
embryonic heart tube development
GO:0035088
establishment or maintenance of apical/basal cell polarity
GO:0036336
dendritic cell migration
GO:0038189
neuropilin signaling pathway
GO:0043410
positive regulation of MAPK cascade
GO:0043525
positive regulation of neuron apoptotic process
GO:0044788
modulation by host of viral process
GO:0045198
establishment of epithelial cell apical/basal polarity
GO:0045740
positive regulation of DNA replication
GO:0046330
positive regulation of JNK cascade
GO:0046847
filopodium assembly
GO:0048549
positive regulation of pinocytosis
GO:0048664
neuron fate determination
GO:0051130
positive regulation of cellular component organization
GO:0051489
regulation of filopodium assembly
GO:0051491
positive regulation of filopodium assembly
GO:0051492
regulation of stress fiber assembly
GO:0051496
positive regulation of stress fiber assembly
GO:0051647
nucleus localization
GO:0051649
establishment of localization in cell
GO:0051683
establishment of Golgi localization
GO:0051835
positive regulation of synapse structural plasticity
GO:0051897
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0051988
regulation of attachment of spindle microtubules to kinetochore
GO:0060047
heart contraction
GO:0060071
Wnt signaling pathway, planar cell polarity pathway
GO:0060501
positive regulation of epithelial cell proliferation involved in lung morphogenesis
GO:0060661
submandibular salivary gland formation
GO:0060997
dendritic spine morphogenesis
GO:0071346
cellular response to type II interferon
GO:0072384
organelle transport along microtubule
GO:0086101
endothelin receptor signaling pathway involved in heart process
GO:0090135
actin filament branching
GO:0090316
positive regulation of intracellular protein transport
GO:0099159
regulation of modification of postsynaptic structure
GO:0099175
regulation of postsynapse organization
GO:1900026
positive regulation of substrate adhesion-dependent cell spreading
Cellular Component
GO:0000139
Golgi membrane
GO:0000322
storage vacuole
GO:0005737
cytoplasm
GO:0005789
endoplasmic reticulum membrane
GO:0005813
centrosome
GO:0005819
spindle
GO:0005829
cytosol
GO:0005856
cytoskeleton
GO:0005886
plasma membrane
GO:0005911
cell-cell junction
GO:0005925
focal adhesion
GO:0016020
membrane
GO:0017119
Golgi transport complex
GO:0030141
secretory granule
GO:0030175
filopodium
GO:0030425
dendrite
GO:0030496
midbody
GO:0031252
cell leading edge
GO:0031256
leading edge membrane
GO:0032991
protein-containing complex
GO:0036464
cytoplasmic ribonucleoprotein granule
GO:0042995
cell projection
GO:0043005
neuron projection
GO:0043025
neuronal cell body
GO:0043197
dendritic spine
GO:0045177
apical part of cell
GO:0045335
phagocytic vesicle
GO:0051233
spindle midzone
GO:0070062
extracellular exosome
GO:0071944
cell periphery
GO:0072686
mitotic spindle
GO:0098685
Schaffer collateral - CA1 synapse
GO:0098794
postsynapse
GO:0098978
glutamatergic synapse
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Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:1a4r
,
PDBe:1a4r
,
PDBj:1a4r
PDBsum
1a4r
PubMed
10211824
UniProt
P60953
|CDC42_HUMAN Cell division control protein 42 homolog (Gene Name=CDC42)
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