SAXSdb — 7ppi

▼

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

Nicotinamide phosphoribosyltransferase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;N-[4-[(5R)-1-(4-azanylbutyl)-6-oxidanylidene-5-quinolin-5-yl-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide ; × 2 PHOSPHATE ION × 2 CHLORIDE ION × 4 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;N-[4-[(5R)-1-(4-azanylbutyl)-6-oxidanylidene-5-quinolin-5-yl-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide ; × 2 PHOSPHATE ION × 2 CHLORIDE ION × 3 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAMPT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–492； UniProt 1–491 Author chain B； PDBConstruct 2–492； UniProt 1–491 Author chain C； PDBConstruct 2–492； UniProt 1–491 Author chain D； PDBConstruct 2–492； UniProt 1–491

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7ppi
Deposition date deposition_date	2021-09-13
Structure title title	Crystal STRUCTURE OF NAMPT IN COMPLEX WITH Compound 11
Keywords keywords	SMALL MOLECULE INHIBITOR, NMPRTASE, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

7ppi__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7ppi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ppi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.78 Å
Rg (electron density)	28.84 Å
Total Rg	29.65 Å
Atom count	7519
Residues	927
Excluded volume	134410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ppi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7ppi__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Nicotinamide phosphoribosyltransferase
Molecular weight formula_weight	55652.0 kDa
EC 编号 ec_number	2.4.2.12
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16184

GMNPAAEAEFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKTENSKLRKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELEAAHH

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;N-[4-[(5R)-1-(4-azanylbutyl)-6-oxidanylidene-5-quinolin-5-yl-4,5-dihydropyridazin-3-yl]phenyl]-1,3-dihydropyrrolo[3,4-c]pyridine-2-carboxamide ;
Molecular weight formula_weight	533.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

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	7

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1146

▶

Unit-cell length a length_a	82.207 Å
Unit-cell length b length_b	106.260 Å
Unit-cell length c length_c	120.955 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	46.140 Å
R factor r_factor	0.2940
R_work r_work	0.2923
R_free r_free	0.3595

Crystal STRUCTURE OF NAMPT IN COMPLEX WITH Compound 11

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

Nicotinamide phosphoribosyltransferase

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

7ppi__assembly_2__model_1

7ppi__assembly_2__model_1 | I(q)

7ppi__assembly_2__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 non-polymer

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)

Crystal STRUCTURE OF NAMPT IN COMPLEX WITH Compound 11

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

Nicotinamide phosphoribosyltransferase

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

7ppi__assembly_2__model_1

7ppi__assembly_2__model_1 | I(q)

7ppi__assembly_2__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 non-polymer

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)