Structure of PDB 5b5p Chain A

Receptor sequence

>5b5pA (length=167) Species: 9606 (Homo sapiens)

YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGHFMLP
DDDVQGIQSLYGPGDED

3D structure

• PDB: 5b5p Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (MMP)-13 Inhibitors with a 1,2,4-Triazol-3-yl Moiety as a Zinc Binding Group Using a Structure-Based Design Approach
• Chain: A
• Resolution: 1.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H222 E223 H226 H232
• Catalytic site (residue number reindexed from 1): H119 E120 H123 H129
• Enzyme Commision number: 3.4.24.-

Interaction with ligand

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	ZN	A	H222 H226 H232	H119 H123 H129
BS02	ZN	A	H172 D174 H187 H200	H69 D71 H84 H97
BS03	CA	A	D179 G180 S182 L184 D202 E205	D76 G77 S79 L81 D99 E102
BS04	CA	A	D162 N194 Y195 G196 D198	D59 N91 Y92 G93 D95
BS05	CA	A	D128 D203 E205	D25 D100 E102
BS06	WNN	A	L218 H222 E223 H226 H232 L239 F241 P242 I243 Y244 T245 T247 F252 P255	L115 H119 E120 H123 H129 L136 F138 P139 I140 Y141 T142 T144 F147 P150	MOAD: ic50=0.2nM PDBbind-CN: -logKd/Ki=9.70,IC50=0.2nM BindingDB: IC50=0.200000nM

Gene Ontology

Molecular Function

• GO:0004222 metalloendopeptidase activity
• GO:0008237 metallopeptidase activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0031012 extracellular matrix

External links

• PDB: RCSB:5b5p, PDBe:5b5p, PDBj:5b5p
• PDBsum: 5b5p
• PubMed: 27966948
• UniProt: P45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)