BioLiP

PDB

5r9d Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.

Chain

Resolution

1.69 Å

3D
structure

Catalytic site residues are labeled in the structure
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Site
#

Ligand

Ligand
chain

Binding residues on receptor
(original residue number in PDB)

Binding residues on receptor
(residue number reindexed from 1)

Binding affinity

BS01

N9J

K53 E71 I84 L104 T106 D168

K46 E64 I77 L97 T99 D160

BS02

N155 D168

N147 D160

Molecular Function

GO:0004672

protein kinase activity

GO:0004674

protein serine/threonine kinase activity

MAP kinase activity

protein binding

ATP binding

kinase activity

enzyme binding

protein phosphatase binding

GO:0048273

mitogen-activated protein kinase p38 binding

GO:0051525

NFAT protein binding

GO:0106310

protein serine kinase activity

	Biological Process
GO:0000077	DNA damage checkpoint signaling
GO:0000165	MAPK cascade
GO:0000902	cell morphogenesis
GO:0001502	cartilage condensation
GO:0001525	angiogenesis
GO:0001649	osteoblast differentiation
GO:0001890	placenta development
GO:0002021	response to dietary excess
GO:0002062	chondrocyte differentiation
GO:0006006	glucose metabolic process
GO:0006355	regulation of DNA-templated transcription
GO:0006357	regulation of transcription by RNA polymerase II
GO:0006366	transcription by RNA polymerase II
GO:0006468	protein phosphorylation
GO:0006915	apoptotic process
GO:0006974	DNA damage response
GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway
GO:0007519	skeletal muscle tissue development
GO:0010628	positive regulation of gene expression
GO:0010831	positive regulation of myotube differentiation
GO:0016310	phosphorylation
GO:0018105	peptidyl-serine phosphorylation
GO:0019395	fatty acid oxidation
GO:0030278	regulation of ossification
GO:0030316	osteoclast differentiation
GO:0031098	stress-activated protein kinase signaling cascade
GO:0031281	positive regulation of cyclase activity
GO:0031663	lipopolysaccharide-mediated signaling pathway
GO:0032495	response to muramyl dipeptide
GO:0032496	response to lipopolysaccharide
GO:0032735	positive regulation of interleukin-12 production
GO:0032868	response to insulin
GO:0035331	negative regulation of hippo signaling
GO:0035556	intracellular signal transduction
GO:0035924	cellular response to vascular endothelial growth factor stimulus
GO:0035994	response to muscle stretch
GO:0038066	p38MAPK cascade
GO:0042307	positive regulation of protein import into nucleus
GO:0042770	signal transduction in response to DNA damage
GO:0045648	positive regulation of erythrocyte differentiation
GO:0045663	positive regulation of myoblast differentiation
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0046323	D-glucose import
GO:0046326	positive regulation of D-glucose import
GO:0048010	vascular endothelial growth factor receptor signaling pathway
GO:0048863	stem cell differentiation
GO:0051146	striated muscle cell differentiation
GO:0051403	stress-activated MAPK cascade
GO:0060045	positive regulation of cardiac muscle cell proliferation
GO:0060348	bone development
GO:0071222	cellular response to lipopolysaccharide
GO:0071223	cellular response to lipoteichoic acid
GO:0071356	cellular response to tumor necrosis factor
GO:0071479	cellular response to ionizing radiation
GO:0071493	cellular response to UV-B
GO:0090090	negative regulation of canonical Wnt signaling pathway
GO:0090336	positive regulation of brown fat cell differentiation
GO:0090400	stress-induced premature senescence
GO:0098586	cellular response to virus
GO:0099179	regulation of synaptic membrane adhesion
GO:1900015	regulation of cytokine production involved in inflammatory response
GO:1901741	positive regulation of myoblast fusion
GO:2000379	positive regulation of reactive oxygen species metabolic process

Biological Process

GO:0000077

DNA damage checkpoint signaling

GO:0000165

MAPK cascade

GO:0000902

cell morphogenesis

GO:0001502

cartilage condensation

GO:0001525

angiogenesis

GO:0001649

osteoblast differentiation

GO:0001890

placenta development

GO:0002021

response to dietary excess

GO:0002062

chondrocyte differentiation

GO:0006006

glucose metabolic process

GO:0006355

regulation of DNA-templated transcription

GO:0006357

regulation of transcription by RNA polymerase II

GO:0006366

transcription by RNA polymerase II

GO:0006468

protein phosphorylation

GO:0006915

apoptotic process

GO:0006974

DNA damage response

GO:0007178

cell surface receptor protein serine/threonine kinase signaling pathway

GO:0007519

skeletal muscle tissue development

GO:0010628

positive regulation of gene expression

GO:0010831

positive regulation of myotube differentiation

GO:0016310

phosphorylation

GO:0018105

peptidyl-serine phosphorylation

GO:0019395

fatty acid oxidation

GO:0030278

regulation of ossification

GO:0030316

osteoclast differentiation

GO:0031098

stress-activated protein kinase signaling cascade

GO:0031281

positive regulation of cyclase activity

GO:0031663

lipopolysaccharide-mediated signaling pathway

GO:0032495

response to muramyl dipeptide

GO:0032496

response to lipopolysaccharide

GO:0032735

positive regulation of interleukin-12 production

GO:0032868

response to insulin

GO:0035331

negative regulation of hippo signaling

GO:0035556

intracellular signal transduction

GO:0035924

cellular response to vascular endothelial growth factor stimulus

GO:0035994

response to muscle stretch

GO:0038066

p38MAPK cascade

GO:0042307

positive regulation of protein import into nucleus

GO:0042770

signal transduction in response to DNA damage

GO:0045648

positive regulation of erythrocyte differentiation

GO:0045663

positive regulation of myoblast differentiation

GO:0045944

positive regulation of transcription by RNA polymerase II

GO:0046323

D-glucose import

GO:0046326

positive regulation of D-glucose import

GO:0048010

vascular endothelial growth factor receptor signaling pathway

GO:0048863

stem cell differentiation

GO:0051146

striated muscle cell differentiation

GO:0051403

stress-activated MAPK cascade

GO:0060045

positive regulation of cardiac muscle cell proliferation

GO:0060348

bone development

GO:0071222

cellular response to lipopolysaccharide

GO:0071223

cellular response to lipoteichoic acid

GO:0071356

cellular response to tumor necrosis factor

GO:0071479

cellular response to ionizing radiation

GO:0071493

cellular response to UV-B

GO:0090090

negative regulation of canonical Wnt signaling pathway

GO:0090336

positive regulation of brown fat cell differentiation

GO:0090400

stress-induced premature senescence

GO:0098586

cellular response to virus

GO:0099179

regulation of synaptic membrane adhesion

GO:1900015

regulation of cytokine production involved in inflammatory response

GO:1901741

positive regulation of myoblast fusion

GO:2000379

positive regulation of reactive oxygen species metabolic process

	Cellular Component
GO:0000922	spindle pole
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005739	mitochondrion
GO:0005829	cytosol
GO:0016607	nuclear speck
GO:0098978	glutamatergic synapse

Cellular Component

spindle pole

nucleus

nucleoplasm

cytoplasm

mitochondrion

cytosol

nuclear speck

glutamatergic synapse

PDB	RCSB:5r9d, PDBe:5r9d, PDBj:5r9d
PDBsum	5r9d
PubMed	32543856
UniProt	P47811\|MK14_MOUSE Mitogen-activated protein kinase 14 (Gene Name=Mapk14)

Structure of PDB 5r9d Chain A