Receptor
PDB id Resolution Class Description Source Keywords
1Y0B 1.8 Å EC: 2.4.2.22 CRYSTAL STRUCTURE OF XANTHINE PHOSPHORIBOSYLTRANSFERASE FROM SUBTILIS. BACILLUS SUBTILIS XANTHINE PURINE METABOLISM PHOSPHORIBOSYLTRANSFERASE STRUGENOMICS PSI PROTEIN STRUCTURE INITATIVE MIDWEST CENTER STRUCTURAL GENOMICS MCSG PROTEIN STRUCTURE INITIATIVE TR
Ref.: CRYSTAL STRUCTURE OF XANTHINE PHOSPHORIBOSYLTRANSFE BACILLUS SUBTILIS TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G4P A:888;
B:888;
C:888;
D:888;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
603.16 C10 H17 N5 O17 P4 c1nc2...
NA A:886;
A:887;
B:886;
B:887;
C:886;
C:887;
D:886;
D:887;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2FXV 2.05 Å EC: 2.4.2.22 BACILLUS SUBTILIS XANTHINE PHOSPHORIBOSYLTRANSFERASE IN COMP GUANOSINE 5'-MONOPHOSPHATE (GMP) BACILLUS SUBTILIS TYPE 1 PHOSPHORIBOSYLTRANSFERASE GMP COMPLEX TRANSFERASE
Ref.: THE EXTRAORDINARY SPECIFICITY OF XANTHINE PHOSPHORIBOSYLTRANSFERASE FROM BACILLUS SUBTILIS EL BY REACTION KINETICS, LIGAND BINDING, AND CRYSTALLO BIOCHEMISTRY V. 45 6615 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1Y0B - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
2 2FXV Kd = 4.5 uM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1Y0B - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
2 2FXV Kd = 4.5 uM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1Y0B - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
2 2FXV Kd = 4.5 uM 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: G4P; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 G4P 1 1
2 0O2 0.905882 1
3 G3D 0.879518 1
4 GDP 0.715909 0.986486
5 3GP 0.674419 0.959459
6 GTP 0.655914 0.986486
7 BGO 0.638889 0.935897
8 GNH 0.634409 0.973333
9 GP3 0.630435 0.960526
10 G G 0.63 0.922078
11 GNP 0.625 0.960526
12 GSP 0.625 0.935897
13 DGI 0.606383 0.935065
14 G 0.604396 0.972973
15 5GP 0.604396 0.972973
16 G1R 0.597938 0.973333
17 GCP 0.597938 0.960526
18 GDD 0.596154 0.948052
19 GDC 0.596154 0.948052
20 GKE 0.596154 0.948052
21 GAV 0.59596 0.948052
22 GPX 0.59 0.959459
23 GPG 0.588235 0.948052
24 GMP 0.588235 0.866667
25 GDP MG 0.57732 0.910256
26 G2P 0.575758 0.948052
27 G G U 0.574074 0.947368
28 GMV 0.571429 0.960526
29 GDP BEF 0.571429 0.8875
30 GH3 0.57 0.986486
31 GGM 0.565217 0.9125
32 2GP 0.565217 0.972973
33 G2R 0.563107 0.948052
34 GFB 0.560748 0.948052
35 GDR 0.560748 0.948052
36 GP2 0.556701 0.948052
37 6CK 0.555556 0.924051
38 ALF 5GP 0.555556 0.876543
39 BEF GDP 0.554455 0.876543
40 GTP MG 0.554455 0.910256
41 DGT 0.55 0.935065
42 GCP G 0.54902 0.922078
43 G A A A 0.547009 0.910256
44 GKD 0.545455 0.948052
45 JB2 0.545455 0.948052
46 CG2 0.543103 0.924051
47 GDX 0.540541 0.960526
48 GPD 0.540541 0.9125
49 GDP AF3 0.538462 0.876543
50 GDP ALF 0.538462 0.876543
51 G G G RPC 0.538462 0.886076
52 G C 0.538462 0.8875
53 Y9Z 0.537037 0.890244
54 G5P 0.536364 0.960526
55 GTG 0.53211 0.924051
56 U A G G 0.529412 0.922078
57 G3A 0.527273 0.960526
58 U2G 0.525862 0.924051
59 APC G U 0.520661 0.897436
60 JB3 0.517241 0.935897
61 YGP 0.513761 0.888889
62 G G G C 0.512195 0.9
63 A G C C 0.508065 0.898734
64 NGD 0.5 0.948052
65 GDP 7MG 0.495575 0.898734
66 DGP 0.494845 0.922078
67 DG 0.494845 0.922078
68 G C C C 0.492188 0.911392
69 P2G 0.489796 0.894737
70 CAG 0.487805 0.869048
71 GPC 0.487805 0.86747
72 2MD 0.487603 0.879518
73 FEG 0.487395 0.86747
74 G U34 0.483333 0.876543
75 ZGP 0.483333 0.857143
76 P1G 0.48 0.883117
77 DBG 0.476562 0.935897
78 MGD 0.475806 0.879518
79 PAP 0.475248 0.918919
80 A G U 0.470588 0.876543
81 U G A 0.467153 0.876543
82 TPG 0.465116 0.829545
83 UCG 0.461538 0.923077
84 MD1 0.460938 0.879518
85 DG DG 0.459459 0.876543
86 G1G 0.456693 0.9125
87 PGD 0.449612 0.9125
88 I2C FE2 CMO CMO 0.448819 0.797753
89 IDP 0.446602 0.959459
90 CGP 0.443548 0.878049
91 G4M 0.442029 0.869048
92 G1R G1R 0.431818 0.911392
93 SGP 0.431373 0.8375
94 FE9 0.430769 0.765957
95 PGD O 0.428571 0.83908
96 DC DG 0.428571 0.855422
97 5GP 5GP 0.424528 0.894737
98 C2E 0.415094 0.933333
99 PCG 0.415094 0.945946
100 35G 0.415094 0.945946
101 AGO 0.414062 0.9
102 MGP 0.40367 0.948052
103 6G0 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2FXV; Ligand: 5GP; Similar sites found: 97
This union binding pocket(no: 1) in the query (biounit: 2fxv.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1QB7 ADE 0.0000288 0.54375 None
2 2D2F ADP 0.002641 0.47015 None
3 1GXU 2HP 0.002396 0.46576 None
4 2IL4 COA 0.008106 0.41128 None
5 2RDK MAN MAN 0.02291 0.40895 None
6 4YDS ATP 0.02629 0.40582 None
7 3F81 STT 0.02719 0.40805 1.0929
8 1XTT U5P 0.0004014 0.47121 1.54639
9 2W58 ADP 0.003369 0.4624 1.54639
10 4GV8 DUP 0.009002 0.40919 1.77515
11 2WE0 UMP 0.001416 0.46054 2.57732
12 2A9W UMP 0.01165 0.42501 2.57732
13 1JJ7 ADP 0.002442 0.4723 3.09278
14 4AG5 ADP 0.009311 0.43269 3.09278
15 2G50 ALA 0.01951 0.41506 3.09278
16 4BQS ADP 0.0191 0.41308 3.40909
17 3P7G MAN 0.03131 0.4032 3.42466
18 1PZM 5GP 0.00003005 0.55036 3.60825
19 3BY9 SIN 0.02033 0.41496 3.60825
20 1JJV ATP 0.03549 0.40058 3.60825
21 4P83 U5P 0.000000469 0.63169 3.84615
22 2X2T GAL NGA 0.01281 0.44098 4.57516
23 2AWN ADP 0.001042 0.4966 4.63918
24 4RHY 3QG 0.00006546 0.49121 4.63918
25 3LRE ADP 0.004397 0.45874 4.63918
26 2CBZ ATP 0.00464 0.45419 4.63918
27 2J5V PCA 0.02172 0.42734 4.63918
28 2NCD ADP 0.01672 0.4192 4.63918
29 3W5J GDP 0.02223 0.41707 4.63918
30 1N62 FAD 0.01048 0.40507 4.63918
31 3P48 DUP 0.007161 0.4216 4.7619
32 1BO4 COA 0.01268 0.41361 4.7619
33 4PPF FLC 0.003359 0.47177 5.15464
34 3B6R CRN 0.009574 0.40953 5.15464
35 3ACC 5GP 0.00001381 0.44329 5.52486
36 4WZ6 ATP 0.007894 0.43723 5.6701
37 4QYS PLR 0.01535 0.40561 5.6701
38 3LN9 FLC 0.002248 0.47468 5.7554
39 1GOJ ADP 0.003771 0.46342 6.18557
40 4IEE AGS 0.00647 0.43264 6.18557
41 3TK1 GDP 0.03149 0.40171 6.18557
42 1G6H ADP 0.00196 0.47856 6.70103
43 3NHB ADP 0.006839 0.44065 6.70103
44 3A4M ADP 0.01014 0.42741 6.92308
45 4KU7 PCG 0.01838 0.40182 7.18954
46 1P18 7HP 0.00004402 0.48415 7.2165
47 1P18 PRP 0.00004402 0.48415 7.2165
48 2XT3 ADP 0.006574 0.44514 7.2165
49 1UPF URF 0.001235 0.42891 7.2165
50 4EIL UMP 0.01352 0.40828 7.2165
51 3IIJ ADP 0.02281 0.40096 7.22222
52 2BES RES 0.009881 0.41485 7.55814
53 2X1L MET 0.009573 0.42789 7.73196
54 1GVF PGH 0.01621 0.41681 7.73196
55 2OBM ADP 0.03615 0.40337 7.73196
56 4QM7 GTP 0.01739 0.40681 8.18713
57 2JBH 5GP 0.00001345 0.56797 8.24742
58 3OZG SSI 0.000002272 0.494 8.24742
59 2OG2 MLI 0.003447 0.44605 8.24742
60 3B9Q MLI 0.01467 0.42093 8.24742
61 4NAE 1GP 0.03294 0.4032 8.24742
62 3W8X FAD 0.01592 0.40263 8.24742
63 2JKY 5GP 0.0003844 0.47721 8.76289
64 1QK3 5GP 0.00008725 0.4741 8.76289
65 5E5U MLI 0.00329 0.40696 8.76289
66 1ECC PCP 0.00002379 0.49498 9.27835
67 1OSS BEN 0.02879 0.40376 9.27835
68 4GQY AMP 0.02197 0.40177 9.69697
69 3RC3 ANP 0.02385 0.40388 10.8247
70 3OBT SLB 0.02819 0.40436 11.3402
71 1YFZ IMP 0.004183 0.44937 11.7073
72 1DQN IMU 0.0002017 0.50867 11.8557
73 2PS1 ORO 0.0000001363 0.66852 12.8866
74 2PS1 PRP 0.000003365 0.54666 12.8866
75 2F6U CIT 0.02102 0.41091 12.8866
76 4CVN ADP 0.01477 0.41892 14.1361
77 2GK6 ADP 0.01064 0.42634 14.433
78 3B5J 12D 0.01229 0.42307 14.433
79 1O5O U5P 0.0001901 0.41498 14.433
80 3UIE ANP 0.01982 0.40399 14.433
81 4K6B GLU 0.03085 0.40218 14.9068
82 1YQT ADP 0.01189 0.42701 15.4639
83 5G5G FAD 0.01579 0.40016 15.4639
84 1HGX 5GP 0.0000133 0.56822 16.3934
85 5JSQ 6MS 0.00001914 0.54519 17.5258
86 4NZ6 DGL 0.01366 0.42382 18.0412
87 5W8V 9YP 0.0001094 0.46811 18.5567
88 1LH0 ORO 0.0002592 0.47992 19.0722
89 1LH0 PRP 0.0002922 0.40496 19.0722
90 3MBI HSX 0.00002077 0.55845 21.6495
91 2WHX ADP 0.005884 0.4429 23.1959
92 1MZV AMP 0.000004753 0.58223 27.3196
93 1ZN7 PRP 0.000001627 0.51603 28.8889
94 1ZN7 ADE 0.000002344 0.46582 28.8889
95 1ZN7 HSX 0.000002344 0.46582 28.8889
96 1L1Q 9DA 0.000001469 0.52322 31.1828
97 1P4A PCP 0.0000006172 0.59256 36.0825
Pocket No.: 2; Query (leader) PDB : 2FXV; Ligand: 5GP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2fxv.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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