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Structure based design of RIP1 kinase inhibitors

Analyse Structure based design of RIP1 kinase inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C4D
Type: protein
Length: 1,057 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor-interacting SERINE/THREONINE-protein kinase 1
EC: 2.7.11.1
UniProt: Q13546
Ligands: EJP
Pockets: 16 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1)	protein	267	41% helix, 15% strand	Q13546
B	Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1)	protein	266	43% helix, 18% strand	Q13546
C	Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1)	protein	258	40% helix, 15% strand	Q13546
D	Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1)	protein	266	37% helix, 15% strand	Q13546

Ligands and binding sites

EJP · (3S)-3-(2-benzyl-3-chloro-7-oxo-2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepine-8-carbonitrile · ligand · 4 copies · chains A, B, C, D

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

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	278	0.76	0.89	37	EJP
2	872	0.76	0.79	85	empty
3	304	0.75	0.87	32	EJP
4	256	0.73	0.87	35	EJP
5	346	0.72	0.84	39	EJP

Interfaces

4 interfaces between chains.

A–C · 451 Å² buried · 1 hydrogen bond · protein-protein
C–D · 254 Å² buried · 1 hydrogen bond · protein-protein
A–B · 163 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 131 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6C4D · Structure based design of RIP1 kinase inhibitors · the same entry in another collection · chain D against D, TM-score 1.00
Q13546 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain D against A, TM-score 0.95

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 Q13546
Elsewhere: RCSB PDB 6C4D · PDBe 6C4D · UniProt Q13546

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