MolNFT v1 · #57268 · protein

Crystal structure of a pyrazolopyrimidine inhibitor complex bound to mapkap kinase-2 (MK2)

3A2C · MAP kinase-activated protein kinase 2: “Crystal structure of a pyrazolopyrimidine inhibitor complex bound to mapkap kinase-2 (MK2)”. X-ray diffraction, 2 ligands (PDY, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #57268 on…

PDB: 3A2C
Type: protein
Length: 3,311 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MAP kinase-activated protein kinase 2
EC: 2.7.11.1
UniProt: P49137
Ligands: PDY, SO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 10 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	274	42% helix, 18% strand	P49137
B	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	277	41% helix, 19% strand	P49137
C	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	273	38% helix, 19% strand	P49137
D	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	277	39% helix, 19% strand	P49137
E, L	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	276	40% helix, 18% strand	P49137
F	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	287	39% helix, 18% strand	P49137
G	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	273	40% helix, 18% strand	P49137
H	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	275	38% helix, 18% strand	P49137
I, J	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	275	40% helix, 19% strand	P49137
K	MAP kinase-activated protein kinase 2 (EC 2.7.11.1)	protein	273	40% helix, 18% strand	P49137

Ligands and binding sites

PDY · N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
SO4 · Sulfate ion · ion · chains F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	186	0.79	0.94	30	empty
2	560	0.78	0.84	57	empty
3	246	0.69	0.85	25	empty
4	747	0.68	0.76	66	empty
5	676	0.68	0.76	68	empty

Interfaces

30 interfaces between chains.

D–F · 890 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 872 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 869 Å² buried · 11 hydrogen bonds · protein-protein
G–I · 860 Å² buried · 10 hydrogen bonds · protein-protein
H–I · 852 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3A2C · Crystal structure of a pyrazolopyrimidine inhibitor complex bound to MAPKAP Kinase-2 (MK2) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P49137
Elsewhere: RCSB PDB 3A2C · PDBe 3A2C · UniProt P49137

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