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Chlorine in PDB 6oi9: Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine

Enzymatic activity of Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine

All present enzymatic activity of Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine:
6.3.4.14; 6.4.1.2;

Protein crystallography data

The structure of Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine, PDB code: 6oi9 was solved by L.D.Andrews, T.R.Kane, P.Dozzo, C.M.Haglund, D.J.Hilderbrandt, M.S.Linsell, T.Machajewski, G.Mcenroe, A.W.Serio, K.B.Wlasichuk, D.B.Neau, S.Pakhomova, G.L.Waldrop, M.Sharp, J.Pogliano, R.Cirz, F.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.25 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.352, 106.782, 122.345, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine (pdb code 6oi9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine, PDB code: 6oi9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6oi9

Go back to Chlorine Binding Sites List in 6oi9
Chlorine binding site 1 out of 4 in the Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:27.1
occ:1.00
 CLY A:MQM501 0.0 27.1 1.0
CAT A:MQM501 1.8 25.0 1.0
CAU A:MQM501 2.7 25.9 1.0
CAS A:MQM501 2.8 24.3 1.0
CAH A:MQM501 3.1 22.8 1.0
CAI A:MQM501 3.4 23.8 1.0
CD2 A:LEU278 3.5 22.1 1.0
NAL A:MQM501 3.5 24.2 1.0
CG A:HIS209 3.6 22.2 1.0
CAP A:MQM501 3.7 26.5 1.0
CD2 A:HIS209 3.8 22.3 1.0
ND1 A:HIS209 3.8 22.6 1.0
CAG A:MQM501 3.8 21.6 1.0
CAV A:MQM501 4.0 25.7 1.0
NE2 A:HIS209 4.0 22.3 1.0
CB A:HIS209 4.0 22.6 1.0
CE1 A:HIS209 4.0 22.5 1.0
CAX A:MQM501 4.1 26.9 1.0
CD1 A:ILE287 4.2 22.3 1.0
CAQ A:MQM501 4.2 26.4 1.0
NAJ A:MQM501 4.3 22.6 1.0
CG2 A:ILE437 4.5 25.8 1.0
CAW A:MQM501 4.5 26.6 1.0
CAM A:MQM501 4.6 25.6 1.0
CD1 A:ILE437 4.7 29.1 1.0
C5 A:MQM501 4.7 21.3 1.0
CA A:HIS209 4.8 22.9 1.0
C4 A:MQM501 4.9 21.9 1.0
CAN A:MQM501 4.9 26.4 1.0
CG A:LEU278 4.9 22.3 1.0
CAO A:MQM501 5.0 26.1 1.0

Chlorine binding site 2 out of 4 in 6oi9

Go back to Chlorine Binding Sites List in 6oi9
Chlorine binding site 2 out of 4 in the Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:30.6
occ:1.00
 CLZ A:MQM501 0.0 30.6 1.0
CAX A:MQM501 1.7 26.9 1.0
CAW A:MQM501 2.7 26.6 1.0
CAS A:MQM501 2.8 24.3 1.0
CAH A:MQM501 3.2 22.8 1.0
O A:HOH820 3.4 45.9 1.0
CAG A:MQM501 3.5 21.6 1.0
CE1 A:HIS236 3.7 34.0 1.0
CE A:MET169 3.8 41.1 1.0
CAV A:MQM501 4.0 25.7 1.0
CAT A:MQM501 4.0 25.0 1.0
CAI A:MQM501 4.0 23.8 1.0
CD1 A:ILE437 4.3 29.1 1.0
CAP A:MQM501 4.3 26.5 1.0
NE2 A:HIS236 4.4 35.3 1.0
CAU A:MQM501 4.5 25.9 1.0
NAL A:MQM501 4.5 24.2 1.0
C5 A:MQM501 4.6 21.3 1.0
ND1 A:HIS236 4.6 32.7 1.0
OH A:TYR203 4.7 30.0 1.0
O A:HOH707 4.8 24.4 1.0
CE1 A:HIS438 4.8 33.0 1.0
O A:HOH795 4.8 41.4 1.0
NAJ A:MQM501 4.9 22.6 1.0

Chlorine binding site 3 out of 4 in 6oi9

Go back to Chlorine Binding Sites List in 6oi9
Chlorine binding site 3 out of 4 in the Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:38.2
occ:1.00
 CLY B:MQM501 0.0 38.2 1.0
CAT B:MQM501 1.7 41.4 1.0
CAU B:MQM501 2.6 42.2 1.0
CAS B:MQM501 2.7 44.0 1.0
CAH B:MQM501 3.0 45.3 1.0
CAI B:MQM501 3.5 47.9 1.0
CD2 B:LEU278 3.5 34.9 1.0
CG B:HIS209 3.7 31.5 1.0
NAL B:MQM501 3.7 48.1 1.0
CD2 B:HIS209 3.8 32.6 1.0
CAG B:MQM501 3.8 46.6 1.0
ND1 B:HIS209 3.8 32.4 1.0
CAV B:MQM501 3.9 43.9 1.0
CAX B:MQM501 4.0 45.7 1.0
NE2 B:HIS209 4.0 33.0 1.0
CE1 B:HIS209 4.0 33.2 1.0
CAP B:MQM501 4.0 48.3 1.0
CB B:HIS209 4.1 30.6 1.0
CAQ B:MQM501 4.1 50.0 1.0
CD1 B:ILE287 4.1 33.3 1.0
NAJ B:MQM501 4.4 46.6 1.0
CAW B:MQM501 4.5 44.1 1.0
CG2 B:ILE437 4.5 32.8 1.0
CAM B:MQM501 4.6 47.8 1.0
CD1 B:ILE437 4.6 37.4 1.0
C5 B:MQM501 4.7 48.1 1.0
O B:HOH643 4.9 24.9 1.0
CAN B:MQM501 4.9 49.3 1.0
CA B:HIS209 4.9 29.1 1.0
CG B:LEU278 4.9 35.9 1.0
C4 B:MQM501 4.9 46.6 1.0

Chlorine binding site 4 out of 4 in 6oi9

Go back to Chlorine Binding Sites List in 6oi9
Chlorine binding site 4 out of 4 in the Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of E. Coli Biotin Carboxylase Complexed with 7-[3- (Aminomethyl)Pyrrolidin-1-Yl]-6-(2,6-Dichlorophenyl)Pyrido[2,3- D]Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:44.2
occ:1.00
 CLZ B:MQM501 0.0 44.2 1.0
CAX B:MQM501 1.7 45.7 1.0
CAW B:MQM501 2.7 44.1 1.0
CAS B:MQM501 2.7 44.0 1.0
CAH B:MQM501 3.0 45.3 1.0
CAG B:MQM501 3.4 46.6 1.0
CE1 B:HIS236 3.6 50.7 1.0
CAI B:MQM501 3.9 47.9 1.0
CE B:MET169 3.9 66.5 1.0
CAT B:MQM501 4.0 41.4 1.0
CAV B:MQM501 4.0 43.9 1.0
CAP B:MQM501 4.1 48.3 1.0
CD1 B:ILE437 4.2 37.4 1.0
NAL B:MQM501 4.3 48.1 1.0
C5 B:MQM501 4.4 48.1 1.0
ND1 B:HIS236 4.5 48.1 1.0
CAU B:MQM501 4.5 42.2 1.0
OH B:TYR203 4.5 54.5 1.0
NE2 B:HIS236 4.6 52.5 1.0
NAJ B:MQM501 4.7 46.6 1.0
CE1 B:HIS438 4.8 42.4 1.0
O B:HOH683 4.8 41.5 1.0

Reference:

L.D.Andrews, T.R.Kane, P.Dozzo, C.M.Haglund, D.J.Hilderbrandt, M.S.Linsell, T.Machajewski, G.Mcenroe, A.W.Serio, K.B.Wlasichuk, D.B.Neau, S.Pakhomova, G.L.Waldrop, M.Sharp, J.Pogliano, R.T.Cirz, F.Cohen. Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase. J.Med.Chem. V. 62 7489 2019.
ISSN: ISSN 0022-2623
PubMed: 31306011
DOI: 10.1021/ACS.JMEDCHEM.9B00625
Page generated: Sat Jul 12 17:50:56 2025

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