2BT4

Type II Dehydroquinase inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb2BT4/pdb

Classification: LYASE
Organism(s): Streptomyces coelicolor
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2005-05-26 Released: 2006-02-13
Deposition Author(s): Toscano, M.D., Stewart, K.A., Coggins, J.R., Lapthorn, A.J., Abell, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Rational Design of New Bifunctional Inhibitors of Type II Dehydroquinase.

Toscano, M.D., Stewart, K.A., Coggins, J.R., Lapthorn, A.J., Abell, C.

(2005) Org Biomol Chem 3: 3102

PubMed: 16106291 Search on PubMed
DOI: https://doi.org/10.1039/b507156a
Primary Citation of Related Structures:
2BT4

PubMed Abstract:
Selective inhibitors of type II dehydroquinase were rationally designed to explore a second binding-pocket in the active-site. The molecular modelling, synthesis, inhibition studies and crystal structure determination are described.

Organizational Affiliation

University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK.

Macromolecule Content

Total Structure Weight: 206.11 kDa
Atom Count: 15,641
Modelled Residue Count: 1,788
Deposited Residue Count: 1,884
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	157	Streptomyces coelicolor	Mutation(s): 0 EC: 4.2.1.10
UniProt
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore P15474 Go to UniProtKB: P15474
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15474
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA2 Query on CA2 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain FA [auth H] SDF format, chain IA [auth I] SDF format, chain LA [auth J] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain DA [auth G] SDF format, chain NA [auth K] SDF format, chain PA [auth L] MOL2 format, chain AA [auth F] MOL2 format, chain FA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain DA [auth G] MOL2 format, chain NA [auth K] MOL2 format, chain PA [auth L]	AA [auth F] DA [auth G] FA [auth H] IA [auth I] LA [auth J] AA [auth F], DA [auth G], FA [auth H], IA [auth I], LA [auth J], M [auth A], NA [auth K], PA [auth L], Q [auth B], S [auth C], U [auth D], X [auth E]	(1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID C₁₆ H₂₂ O₆ SCUFESRLGCQXRX-DCDXPUDHSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain LA [auth J] Focus chain M [auth A] Focus chain NA [auth K] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain X [auth E]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain GA [auth H] SDF format, chain O [auth A] SDF format, chain RA [auth L] SDF format, chain BA [auth F] MOL2 format, chain GA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain RA [auth L] MOL2 format, chain BA [auth F]	BA [auth F], GA [auth H], O [auth A], RA [auth L]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth F] Focus chain GA [auth H] Focus chain O [auth A] Focus chain RA [auth L]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth I] SDF format, chain QA [auth L] SDF format, chain N [auth A] SDF format, chain V [auth D] MOL2 format, chain JA [auth I] MOL2 format, chain QA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain V [auth D]	JA [auth I], N [auth A], QA [auth L], V [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain JA [auth I] Focus chain N [auth A] Focus chain QA [auth L] Focus chain V [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain KA [auth I] SDF format, chain MA [auth J] SDF format, chain OA [auth K] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain T [auth C] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain T [auth C]	CA [auth F] EA [auth G] HA [auth H] KA [auth I] MA [auth J] CA [auth F], EA [auth G], HA [auth H], KA [auth I], MA [auth J], OA [auth K], P [auth A], R [auth B], T [auth C], W [auth D], Y [auth E], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain P [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
CA2	Binding MOAD: 2BT4	Ki: 3.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.616	α = 65.91
b = 196.487	β = 65.91
c = 240.626	γ = 90.01

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-13
Type: Initial release
Version 1.1: 2011-06-09
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description