SAXSdb — 9dtw

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

Dihydropteridine reductase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peptidyl-prolyl cis-trans isomerase FKBP1A × 1 （P62942） GLYCEROL × 1 CHLORIDE ION × 1 ;(2S)-N-[(2R)-1-({[(1R)-6-(4-[(4S)-5,6-dihydro[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl]-6-{[(1S)-3-methyl-1-(1H-1,2,4-triazol-3-yl)butyl]amino}-1,3,5-triazin-2-yl)-6-azaspiro[2.5]octan-1-yl]methyl}amino)-4-(4-methoxyphenyl)-1-oxobutan-2-yl]-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carboxamide ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHPR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–245； UniProt 1–244

Peptidyl-prolyl cis-trans isomerase FKBP1A

Homo sapiens

UniProt P62942

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Dihydropteridine reductase × 1 （P09417） GLYCEROL × 1 CHLORIDE ION × 1 ;(2S)-N-[(2R)-1-({[(1R)-6-(4-[(4S)-5,6-dihydro[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl]-6-{[(1S)-3-methyl-1-(1H-1,2,4-triazol-3-yl)butyl]amino}-1,3,5-triazin-2-yl)-6-azaspiro[2.5]octan-1-yl]methyl}amino)-4-(4-methoxyphenyl)-1-oxobutan-2-yl]-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carboxamide ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FKB1A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–109； UniProt 1–108

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	9dtw
Deposition date deposition_date	2024-10-02
Last revision last_revision	2025-10-08
Structure title title	Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4
Keywords keywords	FKBP12, QDPR, glue degrader, LIGASE; LIGASE
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.

9dtw__assembly_1__model_1

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

Download this curve (.dat)

9dtw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dtw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.72 Å
Rg (electron density)	20.77 Å
Total Rg	21.68 Å
Atom count	5325
Residues	342
Excluded volume	47147 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dtw__assembly_1__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	Dihydropteridine reductase
Molecular weight formula_weight	25873.5 kDa
EC 编号 ec_number	1.5.1.34
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	5732

GMAAAAAAGEARRVLVYGGRGALGSRCVQAFRARNWWVASVDVVENEEASASIIVKMTDSFTEQADQVTAEVGKLLGEEKVDAILCVAGGWAGGNAKSKSLFKNCDLMWKQSIWTSTISSHLATKHLKEGGLLTLAGAKAALDGTPGMIGYGMAKGAVHQLCQSLAGKNSGMPPGAAAIAVLPVTLDTPMNRKSMPEADFSSWTPLEFLVETFHDWITGKNRPSSGSLIQVVTTEGRTELTPAYF

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptidyl-prolyl cis-trans isomerase FKBP1A
Molecular weight formula_weight	12054.8 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SMGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	;(2S)-N-[(2R)-1-({[(1R)-6-(4-[(4S)-5,6-dihydro[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl]-6-{[(1S)-3-methyl-1-(1H-1,2,4-triazol-3-yl)butyl]amino}-1,3,5-triazin-2-yl)-6-azaspiro[2.5]octan-1-yl]methyl}amino)-4-(4-methoxyphenyl)-1-oxobutan-2-yl]-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carboxamide ;
Molecular weight formula_weight	922.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	374

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Unit-cell length a length_a	109.937 Å
Unit-cell length b length_b	61.416 Å
Unit-cell length c length_c	69.971 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.390 Å
Low-resolution limit resolution_low	30.400 Å
R factor r_factor	0.1902
R_work r_work	0.1889
R_free r_free	0.2142

Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4

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

Dihydropteridine reductase

State in the Current Structure

Other States of the Same Protein in the Database

Peptidyl-prolyl cis-trans isomerase FKBP1A

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

9dtw__assembly_1__model_1

9dtw__assembly_1__model_1 | I(q)

9dtw__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4

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

Dihydropteridine reductase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peptidyl-prolyl cis-trans isomerase FKBP1A

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

9dtw__assembly_1__model_1

9dtw__assembly_1__model_1 | I(q)

9dtw__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)