6UDL | pdb_00006udl

Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) ICT-2700

• PDB DOI: https://doi.org/10.2210/pdb6UDL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-19 Released: 2020-09-23 
• Deposition Author(s): Bart, A.G., Scott, E.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Cytochrome P450 binding and bioactivation of tumor-targeted duocarmycin agents

Bart, A.G., Morais, G., Vangala, V.R., Loadman, P.M., Pors, K., Scott, E.E.

(2021) Drug Metab Dispos 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 227 kDa 
• Atom Count: 15,242 
• Modeled Residue Count: 1,877 
• Deposited Residue Count: 1,964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 1A1	A, B, C, D	491	Homo sapiens	Mutation(s): 0  Gene Names: CYP1A1 EC: 1.14.14.1 (PDB Primary Data), 4.2.1.152 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P04798 (Homo sapiens) Explore P04798  Go to UniProtKB:  P04798
PHAROS:  P04798 GTEx:  ENSG00000140465

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B], I [auth C], J [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
Q4M (Subject of Investigation/LOI)	F [auth A], H [auth B]	[(1S)-1-(chloromethyl)-1,6-dihydropyrrolo[3,2-e]indol-3(2H)-yl](5-methoxy-1H-indol-2-yl)methanone C21 H18 Cl N3 O2 ZHFAARVXMYJTEZ-CYBMUJFWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.371	α = 90
b = 196.147	β = 90
c = 237.222	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Bart, A.G., Scott, E.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM076343

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2021-10-13
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Refinement description