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CP2R1_HUMAN_31_501

Vitamin D 25-hydroxylase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2R1_HUMAN):114, 115, 118, 119, 125, 126, 214, 217, 218, 221, 246, 250, 253, 254, 257, 301, 302, 305, 306, 309, 310, 313, 314, 375, 379, 487, 488114, 115, 118, 119, 125, 126, 214, 217, 218, 221, 246, 250, 253, 254, 257, 301, 302, 305, 306, 309, 310, 313, 314, 375, 379, 487, 488
Cofactors (cF):bcd/hem
Metals (Me):Fe

Full PDB list

3c6g, 3czh, 3dl9

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
L
1
1
4
F
1
1
5
M
1
1
8
T
1
1
9
L
1
2
5
N
1
2
6
F
2
1
4
V
2
1
8
A
2
2
1
A
2
5
0
V
2
5
3
Y
2
5
4
L
2
5
7
I
3
0
1
F
3
0
2
G
3
0
5
E
3
0
6
I
3
0
9
E
3
1
3
T
3
1
4
V
3
7
5
I
3
7
9
M
4
8
7
T
4
8
8
[1]3c6g.a vd328 . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3czh.b d2v29 . . . . . . . . . . . . . . . . . . . . . . . . bcd,hem Fe
[1]3dl9.a v2h30 . . . . . . . . . . . . . . . . . . . . . . . . hem Fe

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1 cF Me
L
1
1
4
F
1
1
5
M
1
1
8
T
1
1
9
L
1
2
5
N
1
2
6
F
2
1
4
N
2
1
7
V
2
1
8
A
2
2
1
L
2
4
6
A
2
5
0
V
2
5
3
Y
2
5
4
L
2
5
7
I
3
0
1
F
3
0
2
G
3
0
5
E
3
0
6
I
3
0
9
A
3
1
0
E
3
1
3
T
3
1
4
V
3
7
5
I
3
7
9
M
4
8
7
T
4
8
8
[1]3c6g.a . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3czh.b . . . . . . . . . . . . . . . . . . . . . . . . . . . bcd,hem Fe
[1]3dl9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3c6g.a:vd3
3czh.b:d2v
3dl9.a:v2h
[1] 3c6g.a
0
0 0
[1] 3czh.b 0
0
0
[1] 3dl9.a 0.1 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3c6g.a
3czh.b
3dl9.a
[1] 3c6g.a
0
0 0
[1] 3czh.b 0
0
0
[1] 3dl9.a 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3c6g.a
3czh.b
3dl9.a
[1] 3c6g.a
0
0.2 0.1
[1] 3czh.b 0.2
0
0.2
[1] 3dl9.a 0.1 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3c6g.a
3czh.b
3dl9.a
[1] 3c6g.a
0
0.3 0.1
[1] 3czh.b 0.3
0
0.3
[1] 3dl9.a 0.1 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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