6NGJ: Rat neuronal nitric oxide synthase heme domain

Structure of rat neuronal nitric oxide synthase heme domain in complex with 6-(3-fluoro-5-(3-(methylamino)prop-1-yn-1-yl)phenethyl)-4-methylpyridin-2-amine. Determined by X-ray diffraction at 1.76 Å resolution. Released 13 Mar 2019.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 7,286
Mol. weight: 100.12 kDa
Ligands: ZN, KLY, H4B, HEM
Released: 13 Mar 2019

Explore 6NGJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NGJ contains 53 α-helices and 52 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: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	301-304	4	1
β-strand	305	1	2
β-strand	311-314	4	1
α-helix	316-319	4
β-strand	331	1	3
α-helix	351-368	18
α-helix	375-391	17
α-helix	398-410	13
α-helix	418-420	3
β-strand	425-428	4	4
α-helix	435-450	16
α-helix	451-453	3
β-strand	458-461	4	4
α-helix	462-465	4
β-strand	473-474	2	5
β-strand	478	1	4
β-strand	482	1	6
β-strand	484-486	3	7
β-strand	492-494	3	7
α-helix	496-498	3
α-helix	499-506	8
α-helix	518	1
β-strand	519	1	6
α-helix	520-521	2
β-strand	522-525	4	5
β-strand	532-534	3	5
α-helix	535-537	3
α-helix	538-540	3
β-strand	543-545	3	8
α-helix	554-557	4
β-strand	560-562	3	8
β-strand	566-567	2	4
β-strand	571-574	4	9
β-strand	577-579	3	9
β-strand	584-585	2	4
β-strand	588-589	2	10
α-helix	590-591	2
α-helix	592-597	6
α-helix	598-599	2
α-helix	607-613	7
α-helix	621-623	3
α-helix	625-643	19
β-strand	648-649	2	10
α-helix	651-669	19
α-helix	676-679	4
α-helix	685-687	3
α-helix	689-692	4
β-strand	693	1	2
β-strand	697	1	11
β-strand	703-705	3	9
α-helix	710-712	3

Chain B: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	301-304	4	12
β-strand	305	1	13
β-strand	311-314	4	12
α-helix	316-319	4
β-strand	327	1	14
β-strand	330	1	14
β-strand	331	1	11
α-helix	351-368	18
α-helix	375-391	17
α-helix	398-410	13
α-helix	418-420	3
β-strand	425-428	4	15
α-helix	435-450	16
α-helix	451-453	3
β-strand	458-461	4	15
α-helix	462-465	4
β-strand	473-474	2	16
β-strand	478	1	15
β-strand	482	1	17
β-strand	484-486	3	18
β-strand	492-494	3	18
α-helix	496-498	3
α-helix	499-507	9
α-helix	518	1
β-strand	519	1	17
α-helix	520-521	2
β-strand	522-525	4	16
α-helix	529-531	3
β-strand	532-534	3	16
α-helix	535-537	3
α-helix	538-540	3
β-strand	543-545	3	19
α-helix	552-557	6
β-strand	560-562	3	19
β-strand	566-567	2	15
β-strand	571-574	4	20
β-strand	577-579	3	20
β-strand	584-585	2	15
β-strand	588-589	2	21
α-helix	590-591	2
α-helix	592-597	6
α-helix	598-599	2
α-helix	607-613	7
α-helix	621-623	3
α-helix	625-643	19
β-strand	648-649	2	21
α-helix	651-669	19
α-helix	676-679	4
α-helix	685-687	3
α-helix	689-692	4
β-strand	693	1	13
β-strand	697	1	3
β-strand	703-705	3	20
α-helix	710-712	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nitric oxide synthase, brain	A, B	protein	422	Rattus norvegicus	P29476 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6NGJ_1 Nitric oxide synthase, brain (chains A, B)
CPRFLKVKNWETDVVLTDTLHLKSTLETGCTEHICMGSIMLPSQHTRKPEDVRTKDQLFP
LAKEFLDQYYSSIKRFGSKAHMDRLEEVNKEIESTSTYQLKDTELIYGAKHAWRNASRCV
GRIQWSKLQVFDARDCTTAHGMFNYICNHVKYATNKGNLRSAITIFPQRTDGKHDFRVWN
SQLIRYAGYKQPDGSTLGDPANVQFTEICIQQGWKAPRGRFDVLPLLLQANGNDPELFQI
PPELVLEVPIRHPKFDWFKDLGLKWYGLPAVSNMLLEIGGLEFSACPFSGWYMGTEIGVR
DYCDNSRYNILEEVAKKMDLDMRKTSSLWKDQALVEINIAVLYSFQSDKVTIVDHHSATE
SFIKHMENEYRCRGGCPADWVWIVPPMSGSITPVFHQEMLNYRLTPSFEYQPDPWNTHVW
KG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
KLY	6-(2-{3-fluoro-5-[3-(methylamino)prop-1-yn-1-yl]phenyl}ethyl)-4-methylpyridin-2…	C18 H20 F N3	2
H4B	5,6,7,8-tetrahydrobiopterin	C9 H15 N5 O3	2
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2

Water and common crystallization additives (ACT) are not listed.

Primary citation

Optimization of Blood-Brain Barrier Permeability with Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibitors Having a 2-Aminopyridine Scaffold. Do, H.T., Li, H., Chreifi, G. et al. J Med Chem (2019) 62:2690-2707. DOI 10.1021/acs.jmedchem.8b02032 · PubMed

Other PDB entries of the same protein (UniProt P29476 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QAU 1.25 Å, Unexpected modes of PDZ domain scaffolding revealed by structure of nnos-syntrophin…
6NGM 1.69 Å, Structure of rat neuronal nitric oxide synthase heme domain in complex with…
7UAN 1.7 Å, Structure of rat neuronal nitric oxide synthase R349A heme domain in complex with…
6PN5 1.7 Å, Structure of rat neuronal nitric oxide synthase heme domain in complex with…
4FVY 1.7 Å, Structure of rat nNOS heme domain in complex with N(omega)-hydroxy-…
6AUS 1.7 Å, Structure of rat neuronal nitric oxide synthase heme domain in complex with…
6AUW 1.7 Å, Structure of rat neuronal nitric oxide synthase heme domain in complex with…
7S3Z 1.73 Å, Structure of rat neuronal nitric oxide synthase heme domain in complex with…
3N5W 1.73 Å, Structure of neuronal nitric oxide synthase heme domain in complex with…
5VUN 1.75 Å, Structure of rat neuronal nitric oxide synthase heme domain in complex with…
6PMW 1.75 Å, Structure of rat neuronal nitric oxide synthase heme domain in complex with…
1OM4 1.75 Å, Structure of rat neuronal nos heme domain with L-arginine bound

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