7g3t

Crystal Structure of rat Autotaxin in complex with (2S)-6-chloro-2-[[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino]-2,3-dihydro-1H-indene-4-carbonitrile, i.e. SMILES C1c2cc(cc(C#N)c2C[C@H]1Nc1ncc(cn1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 microM

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 (2R)-6-chloro-2-{[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino}-2,3-dihydro-1H-indene-4-carbonitrile × 1 ZINC ION × 1 SODIUM ION × 1 CALCIUM ION × 2 POTASSIUM ION × 1 ACETATE ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENPP2_RAT
Isoform	Q64610-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–835； UniProt 28–862

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7g3t
Deposition date deposition_date	2023-06-05
Last revision last_revision	2024-12-18
Structure title title	Crystal Structure of rat Autotaxin in complex with (2S)-6-chloro-2-[[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino]-2,3-dihydro-1H-indene-4-carbonitrile, i.e. SMILES C1c2cc(cc(C#N)c2C[C@H]1Nc1ncc(cn1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 microM
Keywords keywords	;HYDROLASE, LYSOPHOSPHATIDIC ACID, LPA, LYSOPHOSPHATIDYLCHOLINE, LPC, SOMATOMEDIN, METASTASIS, NEUROPATHIC PAIN, VASCULAR DEVELOPMENT, NEURAL DEVELOPMENT ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7g3t__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7g3t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7g3t__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.83 Å
Rg (electron density)	30.02 Å
Total Rg	30.79 Å
Atom count	6648
Residues	807
Excluded volume	117660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7g3t__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Molecular weight formula_weight	97343.3 kDa
EC 编号 ec_number	3.1.4.39
Mutation mutation	N53A, N410A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7800

FTASRIKRAEWDEGPPTVLSDSPWTATSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDKVEPKNKLEELNKRLHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYESEIGGRHHHHHHHH

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1397.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(2R)-6-chloro-2-{[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino}-2,3-dihydro-1H-indene-4-carbonitrile
Molecular weight formula_weight	395.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	855

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Unit-cell length a length_a	83.770 Å
Unit-cell length b length_b	91.690 Å
Unit-cell length c length_c	120.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.330 Å
Low-resolution limit resolution_low	72.920 Å
R factor r_factor	0.1372
R_work r_work	0.1353
R_free r_free	0.1715

Crystal Structure of rat Autotaxin in complex with (2S)-6-chloro-2-[[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino]-2,3-dihydro-1H-indene-4-carbonitrile, i.e. SMILES C1c2cc(cc(C#N)c2C[C@H]1Nc1ncc(cn1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 microM

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7g3t__assembly_1__model_1

7g3t__assembly_1__model_1 | I(q)

7g3t__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Crystal Structure of rat Autotaxin in complex with (2S)-6-chloro-2-[[5-(6-oxa-1-azaspiro[3.3]heptane-1-carbonyl)pyrimidin-2-yl]amino]-2,3-dihydro-1H-indene-4-carbonitrile, i.e. SMILES C1c2cc(cc(C#N)c2C[C@H]1Nc1ncc(cn1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 microM

1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7g3t__assembly_1__model_1

7g3t__assembly_1__model_1 | I(q)

7g3t__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)