4cdc

Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phenylphenyl)ethyl)butanamide

Method: X-RAY DIFFRACTION

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

DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 (2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide × 1 CHLORIDE ION × 1 GLYCEROL × 2 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 1 (2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide × 1 CHLORIDE ION × 1 GLYCEROL × 1 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 (2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 (2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide × 1 CHLORIDE ION × 1 GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CATC_HUMAN
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 25–143 Author chain D； PDBConstruct 1–119； UniProt 25–143 Author chain G； PDBConstruct 1–119； UniProt 25–143 Author chain J； PDBConstruct 1–119； UniProt 25–143 Author chain B； PDBConstruct 1–165； UniProt 230–394 Author chain E； PDBConstruct 1–165； UniProt 230–394 Author chain H； PDBConstruct 1–165； UniProt 230–394 Author chain K； PDBConstruct 1–165； UniProt 230–394 Author chain C； PDBConstruct 1–69； UniProt 395–463 Author chain F； PDBConstruct 1–69； UniProt 395–463 Author chain I； PDBConstruct 1–69； UniProt 395–463 Author chain L； PDBConstruct 1–69； UniProt 395–463

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	4cdc
Deposition date deposition_date	2013-10-31
Structure title title	Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phenylphenyl)ethyl)butanamide
Keywords keywords	HYDROLASE, INHIBITOR; 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.

4cdc__assembly_1__model_1

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

Download this curve (.dat)

4cdc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4cdc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.21 Å
Rg (electron density)	20.12 Å
Total Rg	21.11 Å
Atom count	2789
Residues	344
Excluded volume	49396 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4cdc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4cdc__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4cdc__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4cdc__assembly_4__model_1`	trimeric （3）	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 (8)

Entity 1 Entity 1 polymer

Description description	DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
Molecular weight formula_weight	13500.2 kDa
EC 编号 ec_number	3.4.14.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	11421

DTPANCTYLDLLGTWVFQVGSSGSQRDVNCSVMGPQEKKVVVYLQKLDTAYDDLGNSGHFTIIYNQGFEIVLNDYKWFAFFKYKEEGSKVTTYCNETMTGWVHDVLGRNWACFTGKKVG

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 polymer

Description description	DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
Molecular weight formula_weight	18630.0 kDa
EC 编号 ec_number	3.4.14.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

HLPTSWDWRNVHGINFVSPVRNQASCGSCYSFASMGMLEARIRILTNNSQTPILSPQEVVSCSQYAQGCEGGFPYLIAGKYAQDFGLVEEACFPYTGTDSPCKMKEDCFRYYSSEYHYVGGFYGGCNEALMKLELVHHGPMAVAFEVYDDFLHYKKGIYHHTGLR

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 3 Entity 3 polymer

Description description	DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
Molecular weight formula_weight	7583.4 kDa
EC 编号 ec_number	3.4.14.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

DPFNPFELTNHAVLLVGYGTDSASGMDYWIVKNSWGTGWGENGYFRIRRGTDECAIESIAVAATPIPKL

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	(2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide
Molecular weight formula_weight	309.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	311

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4cdca_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.5 — Dipeptidyl peptidase I (cathepsin C), exclusion domain
Family Family family	b.61.5.1 — Dipeptidyl peptidase I (cathepsin C), exclusion domain

Domain ID domain_id	d4cdcd_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.5 — Dipeptidyl peptidase I (cathepsin C), exclusion domain
Family Family family	b.61.5.1 — Dipeptidyl peptidase I (cathepsin C), exclusion domain

Domain ID domain_id	d4cdcg_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.5 — Dipeptidyl peptidase I (cathepsin C), exclusion domain
Family Family family	b.61.5.1 — Dipeptidyl peptidase I (cathepsin C), exclusion domain

Domain ID domain_id	d4cdcj_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.5 — Dipeptidyl peptidase I (cathepsin C), exclusion domain
Family Family family	b.61.5.1 — Dipeptidyl peptidase I (cathepsin C), exclusion domain

CATH v4.4 (12 domains)

Domain ID domain_id	4cdcA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	80 — Cathepsin C, exclusion domain

Domain ID domain_id	4cdcB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4cdcC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	170 — Cysteine proteinases. Chain C

Domain ID domain_id	4cdcD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	80 — Cathepsin C, exclusion domain

Domain ID domain_id	4cdcE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4cdcF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	170 — Cysteine proteinases. Chain C

Domain ID domain_id	4cdcG00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	80 — Cathepsin C, exclusion domain

Domain ID domain_id	4cdcH01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4cdcI00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	170 — Cysteine proteinases. Chain C

Domain ID domain_id	4cdcJ00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	80 — Cathepsin C, exclusion domain

Domain ID domain_id	4cdcK01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4cdcL00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	170 — Cysteine proteinases. Chain C

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Unit-cell length a length_a	84.276 Å
Unit-cell length b length_b	84.276 Å
Unit-cell length c length_c	224.626 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1928
R_work r_work	0.1907
R_free r_free	0.2325

Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phenylphenyl)ethyl)butanamide

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

DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN

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

4cdc__assembly_1__model_1

4cdc__assembly_1__model_1 | I(q)

4cdc__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phenylphenyl)ethyl)butanamide

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

DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN

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

4cdc__assembly_1__model_1

4cdc__assembly_1__model_1 | I(q)

4cdc__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)