4DD8 | pdb_00004dd8

ADAM-8 metalloproteinase domain with bound batimastat

PDB DOI: https://doi.org/10.2210/pdb4DD8/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2012-01-18 Released: 2012-06-06
Deposition Author(s): Hall, T., Shieh, H.S., Day, J.E., Caspers, N., Chrencik, J.E., Williams, J.M., Pegg, L.E., Pauley, A.M., Moon, A.F., Krahn, J.M., Fischer, D.H., Kiefer, J.R., Tomasselli, A.G., Zack, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.255 (Depositor), 0.263 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of human ADAM-8 catalytic domain complexed with batimastat.

Hall, T., Shieh, H.S., Day, J.E., Caspers, N., Chrencik, J.E., Williams, J.M., Pegg, L.E., Pauley, A.M., Moon, A.F., Krahn, J.M., Fischer, D.H., Kiefer, J.R., Tomasselli, A.G., Zack, M.D.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 616-621

PubMed: 22684055 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309112015618
Primary Citation Related Structures:
4DD8

PubMed Abstract:
The role of ADAM-8 in cancer and inflammatory diseases such as allergy, arthritis and asthma makes it an attractive target for drug development. Therefore, the catalytic domain of human ADAM-8 was expressed, purified and crystallized in complex with a hydroxamic acid inhibitor, batimastat. The crystal structure of the enzyme-inhibitor complex was refined to 2.1 Å resolution. ADAM-8 has an overall fold similar to those of other ADAM members, including a central five-stranded β-sheet and a catalytic Zn(2+) ion. However, unique differences within the S1' binding loop of ADAM-8 are observed which might be exploited to confer specificity and selectivity to ADAM-8 competitive inhibitors for the treatment of diseases involving this enzyme.

Organizational Affiliation

Pfizer Inc, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA.

Macromolecule Content

Total Structure Weight: 96.15 kDa
Atom Count: 6,917
Modeled Residue Count: 815
Deposited Residue Count: 832
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disintegrin and metalloproteinase domain-containing protein 8	A, B, C, D	208	Homo sapiens	Mutation(s): 0 Gene Names: ADAM8, MS2 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P78325 (Homo sapiens) Explore P78325 Go to UniProtKB: P78325
PHAROS: P78325 GTEx: ENSG00000151651
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78325
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BAT Query on BAT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	E [auth A], M [auth B], S [auth C], Y [auth D]	4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE C₂₃ H₃₁ N₃ O₄ S₂ XFILPEOLDIKJHX-QYZOEREBSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain G [auth A] SDF format, chain AA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth D]	AA [auth D], G [auth A], O [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain O [auth B] Focus chain U [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain Z [auth D] SDF format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C]	F [auth A], N [auth B], T [auth C], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain CA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain CA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C] mmCIF format, chain CA [auth D]	CA [auth D], I [auth A], Q [auth B], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain W [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain X [auth C] SDF format, chain P [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B]	BA [auth D] DA [auth D] H [auth A] J [auth A] P [auth B] BA [auth D], DA [auth D], H [auth A], J [auth A], P [auth B], R [auth B], V [auth C], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain H [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain H [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.255 (Depositor), 0.263 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.6	α = 90
b = 50.9	β = 102.4
c = 93.5	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2012-06-27
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary