5SXN: Renin

Structure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as renin inhibitors. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,745
Mol. weight: 75.62 kDa
Ligands: NAG, 74U
Released: 2 Nov 2016

Explore 5SXN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5SXN contains 30 α-helices and 67 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
β-strand	8-12	5	2
β-strand	13-15	3	3
β-strand	19-21	3	3
β-strand	22-26	5	4
β-strand	31-38	8	4
β-strand	44-47	4	4
β-strand	48	1	5
α-helix	56-59	4
β-strand	64	1	5
α-helix	66-68	3
β-strand	73-82	10	4
β-strand	87-99	13	4
β-strand	102-113	12	4
α-helix	116-119	4
β-strand	126-129	4	4
α-helix	133-135	3
α-helix	137-139	3
α-helix	140-142	3
α-helix	143-149	7
β-strand	153	1	1
β-strand	157-162	6	2
α-helix	163-165	3
β-strand	174-178	5	2
α-helix	183-185	3
β-strand	186-194	9	2
β-strand	195	1	6
β-strand	202-205	4	6
β-strand	207-210	4	7
β-strand	216	1	7
β-strand	221-225	5	6
β-strand	232-234	3	6
α-helix	236-246	11
β-strand	249-250	2	8
β-strand	255-258	4	8
α-helix	259-264	6
α-helix	265-267	3
β-strand	268-272	5	7
β-strand	275-279	5	7
α-helix	281-284	4
β-strand	285	1	9
β-strand	295-297	3	8
β-strand	298	1	9
β-strand	300-302	3	6
α-helix	305-306	2
β-strand	313-315	3	6
α-helix	317-322	6
β-strand	323-328	6	2
β-strand	333-339	7	2

Chain B: 15 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	10
β-strand	8-12	5	11
β-strand	13-15	3	12
β-strand	19-26	8	12
β-strand	31-38	8	12
β-strand	44-47	4	12
β-strand	48	1	13
α-helix	57-60	4
β-strand	64	1	13
α-helix	66-68	3
β-strand	73-81	9	12
β-strand	88-99	12	12
β-strand	102-111	10	12
α-helix	116-119	4
β-strand	126-129	4	12
α-helix	133-135	3
α-helix	137-139	3
α-helix	140-142	3
α-helix	143-149	7
β-strand	153	1	10
β-strand	157-162	6	11
α-helix	163-165	3
β-strand	174-178	5	11
α-helix	183-185	3
β-strand	186-194	9	11
β-strand	195	1	14
β-strand	202-205	4	14
β-strand	207-210	4	15
β-strand	213-216	4	15
β-strand	221-225	5	14
β-strand	232-234	3	14
α-helix	236-246	11
β-strand	249-250	2	16
β-strand	255-258	4	16
α-helix	259-264	6
α-helix	266-267	2
β-strand	268-272	5	15
β-strand	275-279	5	15
α-helix	281-284	4
β-strand	285	1	17
β-strand	295-297	3	16
β-strand	298	1	17
β-strand	300-302	3	14
α-helix	305-306	2
β-strand	313-315	3	14
α-helix	317-322	6
β-strand	323-328	6	11
β-strand	333-339	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Renin	A, B	protein	339	Homo sapiens	P00797 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5SXN_1 Renin (chains A, B)
TLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYH
KLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFML
AEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGS
DPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEK
LMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIH
AMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
74U	N-[(furan-2-yl)methyl]-2-phenylquinazolin-4-amine	C19 H15 N3 O	1

Water and common crystallization additives (PGE, PEG) are not listed.

Primary citation

Structure-based design of a new series of N-(piperidin-3-yl)pyrimidine-5-carboxamides as renin inhibitors. Imaeda, Y., Tawada, M., Suzuki, S. et al. Bioorg Med Chem (2016) 24:5771-5780. DOI 10.1016/j.bmc.2016.09.030 · PubMed

Other PDB entries of the same protein (UniProt P00797 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3K1W 1.5 Å, New Classes of Potent and Bioavailable Human Renin Inhibitors
1HRN 1.8 Å, High resolution crystal structures of recombinant human renin in complex with…
2G24 1.9 Å, Ketopiperazine-Based Renin Inhibitors: Optimization of the "C" Ring
2IKO 1.9 Å, Crystal Structure of Human Renin Complexed with Inhibitor
3G72 1.9 Å, Design and Preparation of Potent, Non-Peptidic, Bioavailable Renin Inhibitors
3KM4 1.9 Å, Optimization of Orally Bioavailable Alkyl Amine Renin Inhibitors
3G6Z 2.0 Å, Design and Preparation of Potent, Non-Peptidic, Bioavailable Renin Inhibitors
3G70 2.0 Å, Design and Preparation of Potent, Non-Peptidic, Bioavailable Renin Inhibitors
3GW5 2.0 Å, Crystal structure of human renin complexed with a novel inhibitor
3OWN 2.0 Å, Potent macrocyclic renin inhibitors
4Q1N 2.09 Å, Structure-based design of 4-hydroxy-3,5-substituted piperidines as direct renin inhibitors
2G26 2.1 Å, Ketopiperazine-Based Renin Inhibitors: Optimization of the "C" Ring

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