5KOT: Renin

Discovery of TAK-272: A Novel, Potent and Orally Active Renin In-hibitor. Determined by X-ray diffraction at 2.1 Å resolution. Released 5 Jul 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,583
Mol. weight: 77.14 kDa
Ligands: NAG, 6VU
Released: 5 Jul 2017

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

Secondary structure: helices and β-sheets

5KOT contains 28 α-helices and 63 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: 14 helices, 32 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	56-60	5
β-strand	64	1	5
α-helix	66-68	3
β-strand	73-83	11	4
β-strand	86-99	14	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
β-strand	174-178	5	2
α-helix	183-185	3
β-strand	186-194	9	2
β-strand	202-210	9	6
β-strand	213-216	4	6
β-strand	221-225	5	6
β-strand	232-234	3	6
α-helix	236-246	11
α-helix	248	1
β-strand	249-250	2	7
β-strand	255-258	4	7
α-helix	259-264	6
α-helix	265-267	3
β-strand	268-272	5	6
β-strand	275-279	5	6
α-helix	281-284	4
β-strand	285	1	8
β-strand	295-297	3	7
β-strand	298	1	8
β-strand	300-302	3	6
β-strand	313-315	3	6
α-helix	317-320	4
β-strand	323-328	6	2
β-strand	333-339	7	2

Chain B: 14 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	9
β-strand	8-15	8	10
β-strand	19-26	8	10
β-strand	31-38	8	10
β-strand	44-47	4	10
β-strand	48	1	11
α-helix	56-60	5
β-strand	64	1	11
α-helix	66-68	3
β-strand	73-83	11	10
β-strand	86-99	14	10
β-strand	102-113	12	10
α-helix	116-119	4
β-strand	126-129	4	10
α-helix	133-135	3
α-helix	137-139	3
α-helix	140-142	3
α-helix	143-150	8
β-strand	153	1	9
β-strand	157-162	6	10
β-strand	174-178	5	10
α-helix	183-185	3
β-strand	186-194	9	10
β-strand	195	1	12
β-strand	202-210	9	12
β-strand	213-216	4	12
β-strand	221-225	5	12
β-strand	232-234	3	12
α-helix	236-246	11
β-strand	249-250	2	13
β-strand	255-258	4	13
α-helix	259-264	6
α-helix	266-267	2
β-strand	268-272	5	12
β-strand	275-279	5	12
α-helix	281-284	4
β-strand	285	1	14
β-strand	295-297	3	13
β-strand	298	1	14
β-strand	300-302	3	12
α-helix	305-306	2
β-strand	313-315	3	12
α-helix	317-322	6
β-strand	323-328	6	10
β-strand	333-339	7	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Renin	A, B	protein	337	Homo sapiens	P00797 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5KOT_1 Renin (chains A, B)
GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKL
FDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAE
FDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDP
QHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLM
EALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAM
DIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
6VU	1-(4-methoxybutyl)-~{N}-(2-methylpropyl)-~{N}-[(3~{S},5~{R})-5-morpholin-4-ylca…	C27 H41 N5 O4	2

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

Primary citation

Discovery of TAK-272: A Novel, Potent and Orally Active Renin Inhibitor. Imaeda, Y., Tokuhara, H., Fukase, Y. et al. To be published.

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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