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Calcium in PDB 5b5p: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide, PDB code: 5b5p was solved by H.Oki, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.84 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.798, 36.281, 96.382, 90.00, 130.14, 90.00
R / Rfree (%) 17.3 / 20.8

Other elements in 5b5p:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide (pdb code 5b5p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide, PDB code: 5b5p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5b5p

Go back to Calcium Binding Sites List in 5b5p
Calcium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:16.9
occ:1.00
 O A:LEU184 2.2 20.4 1.0
O A:GLY180 2.2 20.0 1.0
OE2 A:GLU205 2.2 23.1 1.0
OD2 A:ASP202 2.3 15.9 1.0
O A:SER182 2.3 20.8 1.0
OD1 A:ASP179 2.3 19.1 1.0
C A:LEU184 3.4 20.0 1.0
C A:GLY180 3.4 19.1 1.0
C A:SER182 3.4 24.1 1.0
CD A:GLU205 3.4 25.1 1.0
CG A:ASP202 3.4 14.8 1.0
CG A:ASP179 3.5 23.7 1.0
N A:LEU184 3.9 21.2 1.0
N A:SER182 3.9 25.5 1.0
N A:GLY180 4.0 19.0 1.0
C A:PRO181 4.1 24.7 1.0
OD2 A:ASP179 4.1 24.1 1.0
CA A:LEU184 4.1 21.8 1.0
C A:GLY183 4.2 21.3 1.0
CA A:SER182 4.2 26.0 1.0
CB A:ASP202 4.2 15.4 1.0
CG A:GLU205 4.3 19.4 1.0
N A:ASP179 4.3 18.9 1.0
C A:ASP179 4.3 20.6 1.0
OD1 A:ASP202 4.3 16.0 1.0
OE1 A:GLU205 4.3 25.8 1.0
CA A:GLY180 4.3 20.9 1.0
N A:PRO181 4.4 20.8 1.0
O A:PRO181 4.4 25.6 1.0
N A:LEU185 4.4 18.8 1.0
N A:GLY183 4.4 23.0 1.0
CA A:PRO181 4.5 23.3 1.0
CB A:LEU184 4.6 22.9 1.0
CA A:GLY183 4.6 21.7 1.0
O A:HOH406 4.6 41.8 1.0
CA A:LEU185 4.6 18.8 1.0
CA A:ASP179 4.6 21.2 1.0
CB A:ASP179 4.7 20.2 1.0
O A:GLY183 4.7 21.5 1.0
O A:HOH476 4.7 35.3 1.0
O A:ASP179 4.8 20.1 1.0

Calcium binding site 2 out of 6 in 5b5p

Go back to Calcium Binding Sites List in 5b5p
Calcium binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:24.2
occ:1.00
 O A:HOH408 2.3 22.8 1.0
O A:ASN194 2.4 28.6 1.0
O A:GLY196 2.4 21.8 1.0
OD1 A:ASP198 2.4 20.6 1.0
O A:ASP162 2.4 22.2 1.0
O A:HOH447 2.6 24.4 1.0
CG A:ASP198 3.4 22.9 1.0
C A:GLY196 3.5 21.3 1.0
C A:ASP162 3.5 20.3 1.0
C A:ASN194 3.6 30.5 1.0
OD2 A:ASP198 3.9 25.5 1.0
C A:TYR195 3.9 26.5 1.0
N A:GLY196 4.0 23.9 1.0
O A:TYR195 4.0 24.3 1.0
O A:HOH426 4.1 30.8 1.0
O A:ALA161 4.1 20.8 1.0
N A:ASP198 4.1 17.9 1.0
CA A:GLY196 4.3 22.3 1.0
CA A:ASP162 4.3 19.8 1.0
O A:HOH589 4.3 44.8 1.0
CA A:TYR195 4.4 29.7 1.0
N A:TYR195 4.4 30.8 1.0
O A:GLY192 4.5 29.2 1.0
N A:GLY197 4.5 20.2 1.0
N A:ILE163 4.5 18.5 1.0
CA A:ASN194 4.6 33.9 1.0
CB A:ASP198 4.6 20.1 1.0
CA A:GLY197 4.6 19.3 1.0
C A:GLY197 4.7 19.4 1.0
N A:MET164 4.7 18.3 1.0
O A:HOH451 4.7 27.6 1.0
N A:ASN194 4.7 34.4 1.0
CA A:ILE163 4.7 19.4 1.0
CG A:MET164 4.7 17.3 1.0
CA A:ASP198 4.8 18.9 1.0
CH2 A:TRP113 4.8 24.4 1.0
C A:PRO193 4.9 35.0 1.0

Calcium binding site 3 out of 6 in 5b5p

Go back to Calcium Binding Sites List in 5b5p
Calcium binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:49.5
occ:1.00
 O A:GLU205 2.6 20.9 1.0
OD1 A:ASP203 2.7 22.6 1.0
OD2 A:ASP128 2.8 27.4 1.0
O A:ASP203 2.8 18.0 1.0
CG A:ASP128 3.4 27.3 1.0
OD1 A:ASP128 3.4 30.4 1.0
C A:ASP203 3.6 18.4 1.0
OG1 A:THR126 3.8 18.2 1.0
CG A:ASP203 3.8 22.6 1.0
C A:GLU205 3.8 18.4 1.0
O A:HOH464 3.9 38.1 1.0
CA A:ASP203 4.1 18.5 1.0
CD A:PRO127 4.3 15.3 1.0
CD1 A:TRP207 4.3 16.0 1.0
CB A:ASP203 4.4 19.6 1.0
N A:GLU205 4.4 17.9 1.0
N A:ASP204 4.5 16.8 1.0
C A:ASP204 4.6 19.6 1.0
CA A:THR206 4.7 17.5 1.0
N A:THR206 4.7 18.1 1.0
CB A:ASP128 4.7 18.2 1.0
CA A:ASP204 4.7 18.6 1.0
OD2 A:ASP203 4.8 23.1 1.0
CA A:GLU205 4.8 17.6 1.0
NE1 A:TRP207 4.8 15.7 1.0
CG A:PRO127 4.9 15.5 1.0

Calcium binding site 4 out of 6 in 5b5p

Go back to Calcium Binding Sites List in 5b5p
Calcium binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:18.1
occ:1.00
 O B:GLY180 2.2 19.9 1.0
O B:LEU184 2.2 21.3 1.0
OD2 B:ASP202 2.3 18.6 1.0
OE2 B:GLU205 2.3 24.6 1.0
O B:SER182 2.3 22.9 1.0
OD1 B:ASP179 2.3 20.1 1.0
C B:LEU184 3.4 19.0 1.0
C B:GLY180 3.4 22.3 1.0
CG B:ASP202 3.5 19.4 1.0
CD B:GLU205 3.5 23.8 1.0
C B:SER182 3.5 25.8 1.0
CG B:ASP179 3.5 22.1 1.0
N B:LEU184 3.9 21.6 1.0
N B:SER182 3.9 25.1 1.0
N B:GLY180 4.0 21.4 1.0
C B:PRO181 4.1 25.0 1.0
OD2 B:ASP179 4.1 23.8 1.0
CA B:LEU184 4.2 20.5 1.0
CB B:ASP202 4.2 15.2 1.0
C B:GLY183 4.2 22.9 1.0
CA B:SER182 4.2 26.4 1.0
C B:ASP179 4.3 22.5 1.0
CG B:GLU205 4.3 19.7 1.0
N B:ASP179 4.3 20.8 1.0
CA B:GLY180 4.3 21.9 1.0
OE1 B:GLU205 4.3 22.7 1.0
OD1 B:ASP202 4.4 17.9 1.0
N B:PRO181 4.4 23.6 1.0
CA B:PRO181 4.4 25.0 1.0
O B:HOH406 4.4 33.3 1.0
N B:LEU185 4.4 17.5 1.0
N B:GLY183 4.5 22.9 1.0
O B:PRO181 4.5 24.7 1.0
CA B:LEU185 4.5 18.2 1.0
CA B:ASP179 4.6 22.5 1.0
CA B:GLY183 4.6 21.6 1.0
CB B:LEU184 4.6 21.1 1.0
CB B:ASP179 4.7 24.0 1.0
O B:GLY183 4.7 22.1 1.0
O B:ASP179 4.7 22.3 1.0

Calcium binding site 5 out of 6 in 5b5p

Go back to Calcium Binding Sites List in 5b5p
Calcium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:18.8
occ:1.00
 O B:GLY196 2.3 18.8 1.0
O B:ASN194 2.3 22.9 1.0
O B:ASP162 2.4 17.8 1.0
O B:HOH489 2.4 19.0 1.0
O B:HOH433 2.4 19.2 1.0
OD1 B:ASP198 2.4 18.0 1.0
CG B:ASP198 3.4 20.0 1.0
C B:GLY196 3.5 18.2 1.0
C B:ASP162 3.5 17.8 1.0
C B:ASN194 3.5 24.9 1.0
OD2 B:ASP198 3.9 21.4 1.0
C B:TYR195 3.9 22.2 1.0
N B:GLY196 4.0 20.6 1.0
O B:TYR195 4.1 21.4 1.0
O B:HOH435 4.1 28.4 1.0
O B:ALA161 4.1 18.8 1.0
N B:ASP198 4.1 18.8 1.0
CA B:ASP162 4.2 17.4 1.0
CA B:GLY196 4.3 18.0 1.0
O B:HOH544 4.3 45.5 1.0
N B:ASN194 4.4 24.5 1.0
O B:GLY192 4.4 26.9 1.0
CA B:ASN194 4.4 26.4 1.0
N B:TYR195 4.4 22.9 1.0
N B:GLY197 4.5 18.5 1.0
CA B:TYR195 4.5 23.2 1.0
N B:ILE163 4.5 16.0 1.0
CA B:GLY197 4.6 18.8 1.0
CB B:ASP198 4.6 17.8 1.0
O B:HOH468 4.6 24.4 1.0
C B:GLY197 4.7 19.7 1.0
N B:MET164 4.7 16.8 1.0
CA B:ILE163 4.7 16.7 1.0
C B:PRO193 4.7 24.9 1.0
CA B:ASP198 4.8 17.4 1.0
CG B:MET164 4.8 15.6 1.0
CH2 B:TRP113 4.9 22.3 1.0
O B:PRO193 5.0 24.0 1.0

Calcium binding site 6 out of 6 in 5b5p

Go back to Calcium Binding Sites List in 5b5p
Calcium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:50.3
occ:1.00
 OD2 B:ASP128 2.6 27.7 1.0
O B:GLU205 2.7 22.1 1.0
OD1 B:ASP203 2.8 24.6 1.0
O B:ASP203 2.9 19.8 1.0
CG B:ASP128 3.3 25.8 1.0
OD1 B:ASP128 3.5 30.8 1.0
O B:HOH566 3.6 47.0 1.0
C B:ASP203 3.7 18.7 1.0
OG1 B:THR126 3.7 17.8 1.0
CG B:ASP203 3.8 22.3 1.0
O B:HOH498 3.9 35.9 1.0
C B:GLU205 3.9 20.5 1.0
CA B:ASP203 4.1 18.2 1.0
CD B:PRO127 4.3 17.3 1.0
CD1 B:TRP207 4.3 16.7 1.0
CB B:ASP203 4.4 19.1 1.0
CB B:ASP128 4.5 22.1 1.0
N B:GLU205 4.6 19.9 1.0
CA B:THR206 4.6 19.3 1.0
N B:ASP204 4.6 17.1 1.0
OD2 B:ASP203 4.7 23.6 1.0
N B:THR206 4.7 19.0 1.0
C B:ASP204 4.8 20.1 1.0
NE1 B:TRP207 4.8 18.6 1.0
CG B:PRO127 4.9 17.4 1.0
CA B:ASP204 4.9 19.3 1.0
CA B:GLU205 4.9 19.2 1.0
N B:TRP207 4.9 17.7 1.0
N B:ASP128 5.0 18.8 1.0

Reference:

H.Nara, A.Kaieda, K.Sato, T.Naito, H.Mototani, H.Oki, Y.Yamamoto, H.Kuno, T.Santou, N.Kanzaki, J.Terauchi, O.Uchikawa, M.Kori. Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (Mmp)-13 Inhibitors with A 1,2,4-Triazol-3-Yl Moiety As A Zinc Binding Group Using A Structure-Based Design Approach J. Med. Chem. V. 60 608 2017.
ISSN: ISSN 1520-4804
PubMed: 27966948
DOI: 10.1021/ACS.JMEDCHEM.6B01007
Page generated: Sun Jul 14 16:49:58 2024

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