Receptor
PDB id Resolution Class Description Source Keywords
4PTN 1.99 Å EC: 4.1.2.- CRYSTAL STRUCTURE OF YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX MAGNESIUM CATION COORDINATED L-GLYCERALDEHYDE ESCHERICHIA COLI TIM BARREL NAL SUPERFAMILY ALDOLASE CLASS I METAL COORDINLYASE STEREOSPECIFICITY
Ref.: CRYSTAL STRUCTURE OF YAGE, A PUTATIVE DHDPS-LIKE PR FROM ESCHERICHIA COLI K12. PROTEINS V. 71 2102 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:404;
C:405;
D:404;
B:407;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
GXV D:403;
B:406;
C:404;
A:403;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
90.078 C3 H6 O3 C(C(C...
EDO D:402;
A:402;
C:401;
D:401;
A:401;
B:401;
C:403;
B:403;
B:402;
C:402;
B:404;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
PYR B:408;
D:405;
Valid;
Valid;
none;
none;
submit data
88.062 C3 H4 O3 CC(=O...
GOL B:405;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4PTN 1.99 Å EC: 4.1.2.- CRYSTAL STRUCTURE OF YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX MAGNESIUM CATION COORDINATED L-GLYCERALDEHYDE ESCHERICHIA COLI TIM BARREL NAL SUPERFAMILY ALDOLASE CLASS I METAL COORDINLYASE STEREOSPECIFICITY
Ref.: CRYSTAL STRUCTURE OF YAGE, A PUTATIVE DHDPS-LIKE PR FROM ESCHERICHIA COLI K12. PROTEINS V. 71 2102 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PTN - GXV C3 H6 O3 C(C(C=O)O)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4PTN - GXV C3 H6 O3 C(C(C=O)O)....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4PTN - GXV C3 H6 O3 C(C(C=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GXV; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 3GR 1 1
2 GXV 1 1
3 RB5 0.4 0.809524
4 XLS 0.4 0.809524
5 ROR 0.4 0.809524
Ligand no: 2; Ligand: PYR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 KIV 0.411765 0.785714
5 AAE 0.411765 0.625
6 2KT 0.411765 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4ptn.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found: 30
This union binding pocket(no: 2) in the query (biounit: 4ptn.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NZY BCA 0.03758 0.40458 1.48699
2 1JXZ BCA 0.04477 0.40023 1.48699
3 2I6A 5I5 0.02245 0.40445 1.73913
4 4ZH7 FUC GAL NAG GAL FUC 0.01004 0.41259 1.74927
5 4W6Z 8ID 0.01902 0.42701 2.04082
6 1YP4 ADP 0.02516 0.40157 2.33236
7 2Z8G GLC GLC BGC 0.0224 0.40093 3.207
8 2V6A CAP 0.01233 0.41821 3.57143
9 1UZD CAP 0.01272 0.4196 3.73134
10 1RY2 AMP 0.01859 0.4028 3.79009
11 2BJK NAD 0.0455 0.40687 4.66472
12 4O8A FAD 0.005115 0.45365 5.24781
13 1XIM XYL 0.01038 0.41107 5.8309
14 4QDC ASD 0.01236 0.41436 6.41399
15 4IF4 BEF 0.003686 0.42199 8.17308
16 4A0M NAD 0.02499 0.4161 9.62099
17 2QUN FUD 0.01993 0.40429 11.0345
18 5XSS XYP 0.004363 0.4256 11.0759
19 1RBL CAP 0.01425 0.41861 12.844
20 1FDJ 13P 0.0022 0.42558 14.8688
21 1FDJ 2FP 0.007746 0.42106 14.8688
22 1WDD CAP 0.01171 0.42078 28.9062
23 3FGZ BEF 0.01278 0.40603 31.25
24 4IMG NGF 0.000003577 0.45854 36.8601
25 4BWL MN9 0.0002122 0.48583 38.1924
26 2WPB ZZI 0.002288 0.42707 38.484
27 1F74 NAY 0.0002103 0.50411 40.6143
28 3I7S PYR 0.004655 0.42001 40.7534
29 1W3T 3GR 0.000003125 0.60467 41.1079
30 5KZD RCJ 0.001058 0.46738 44.7099
Pocket No.: 3; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4ptn.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4PTN; Ligand: PYR; Similar sites found: 35
This union binding pocket(no: 4) in the query (biounit: 4ptn.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ZQ6 ADP ALF 0.04101 0.40797 1.85185
2 5LRT ADP 0.03817 0.40939 2.33236
3 4J75 TYM 0.03292 0.40672 2.33236
4 154L NAG NAG NAG 0.01102 0.42205 2.7027
5 2EFX NFA 0.01984 0.40875 2.91545
6 5WRJ A3P 0.01815 0.41379 2.9703
7 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.03525 0.40431 3.207
8 1YC5 NCA 0.01941 0.40144 3.25203
9 4DVE BTN 0.004321 0.43942 3.53535
10 3B6Z CO7 0.04055 0.40786 3.79009
11 2FSH ANP 0.005503 0.43573 4.08163
12 4IJP 1EH 0.01802 0.4198 4.08163
13 1KQN NAD 0.02035 0.42137 4.30108
14 1S7G APR 0.02491 0.41004 4.34783
15 4CNG SAH 0.02337 0.40764 4.37318
16 1MWH GTG 0.005149 0.41831 4.66472
17 3HRD FAD 0.04569 0.41367 5.06757
18 2QRD ATP 0.01996 0.40515 5.15464
19 4HP0 NOJ NAG NAG NAG 0.03014 0.41517 5.42636
20 1ZGD NAP 0.02566 0.40266 5.44872
21 2H5Z CTO 0.01032 0.41325 5.7377
22 3BK2 U5P 0.01482 0.41685 5.8309
23 4IGQ THR M3L GLN 0.02017 0.40996 5.8309
24 3ZIU LSS 0.03061 0.40456 5.8309
25 1P6O HPY 0.008761 0.41466 6.8323
26 4DO1 ANN 0.007075 0.42784 6.99708
27 1HFE CYS 0.001498 0.44108 7.31707
28 3PNL ADP 0.03022 0.40673 7.58294
29 1MID LAP 0.01678 0.4056 7.69231
30 5BV3 M7G 0.006851 0.44096 9.0379
31 4B7H NDP 0.02649 0.40963 9.0379
32 4A91 GLU 0.01154 0.40168 9.39597
33 2JFN GLU 0.01831 0.40137 10.1754
34 4LX0 BEF GDP 0.00832 0.45051 11.3703
35 2W1A TSA 0.01038 0.40816 13.3333
Pocket No.: 5; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4ptn.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4PTN; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4ptn.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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