Receptor
PDB id Resolution Class Description Source Keywords
2PHN 1.35 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF AN AMIDE BOND FORMING F420-GAMMA GLUTAM FROM ARCHAEOGLOBUS FULGIDUS ARCHAEOGLOBUS FULGIDUS DSM 4304 GAMMA-GLUTAMYL LIGASE COENZYME F420 BIOSYNTHESIS AMIDE BONENZYME METAL DEPENDENT NEW FOLD GDP BINDING MCSG STRUCGENOMICS PSI-2 PROTEIN STRUCTURE INITIATIVE MIDWEST CENTSTRUCTURAL GENOMICS LIGASE
Ref.: STRUCTURE OF AN AMIDE BOND FORMING F(420):GAMMAGAMMA-GLUTAMYL LIGASE FROM ARCHAEOGLOBU FULGIDUS - A MEMBER OF A NEW FAMILY OF NON-RIBOSOMA SYNTHASES. J.MOL.BIOL. V. 372 456 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:3001;
A:3002;
A:3003;
B:3001;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
EDO A:1001;
A:1002;
A:1003;
A:1004;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GDP A:2696;
B:2697;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
GOL A:4001;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MN A:2001;
A:2002;
B:2001;
B:2002;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PHN 1.35 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF AN AMIDE BOND FORMING F420-GAMMA GLUTAM FROM ARCHAEOGLOBUS FULGIDUS ARCHAEOGLOBUS FULGIDUS DSM 4304 GAMMA-GLUTAMYL LIGASE COENZYME F420 BIOSYNTHESIS AMIDE BONENZYME METAL DEPENDENT NEW FOLD GDP BINDING MCSG STRUCGENOMICS PSI-2 PROTEIN STRUCTURE INITIATIVE MIDWEST CENTSTRUCTURAL GENOMICS LIGASE
Ref.: STRUCTURE OF AN AMIDE BOND FORMING F(420):GAMMAGAMMA-GLUTAMYL LIGASE FROM ARCHAEOGLOBU FULGIDUS - A MEMBER OF A NEW FAMILY OF NON-RIBOSOMA SYNTHASES. J.MOL.BIOL. V. 372 456 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 2PHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 2PHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 2PHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 153
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PHN; Ligand: GDP; Similar sites found: 80
This union binding pocket(no: 1) in the query (biounit: 2phn.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OVZ P85 0.01952 0.41638 None
2 4WXJ GLU 0.0288 0.40375 None
3 1PTR PRB 0.03332 0.40025 None
4 1RTW MP5 0.03379 0.40009 None
5 4Z4P SAH 0.01189 0.40361 1.20482
6 3Q9L ATP 0.0006116 0.45814 2.3622
7 5J1J ANP 0.005446 0.40223 2.3622
8 3TKI S25 0.02048 0.40172 2.3622
9 4BHN BH9 0.008391 0.40046 2.3622
10 1G3Q ADP 0.004093 0.43329 2.53165
11 2C5S AMP 0.007527 0.42932 2.75591
12 3KRR DQX 0.01272 0.41739 2.75591
13 4NZ6 DLY 0.02089 0.40853 2.75591
14 2GZ3 NAP 0.01642 0.40603 2.75591
15 5N49 8LW 0.032 0.40134 2.96296
16 2ZL4 ALA ALA ALA ALA 0.03062 0.40235 3.06122
17 2ZV2 609 0.003877 0.43901 3.14961
18 4OH4 ANP 0.005075 0.41688 3.14961
19 1BZL FAD 0.03307 0.41278 3.14961
20 2WPF WPF 0.04291 0.40807 3.14961
21 2NUN ADP 0.02081 0.4069 3.14961
22 2WPF FAD 0.04467 0.40601 3.14961
23 5TPC GAL SIA NGA GAL SIA 0.03496 0.40237 3.14961
24 3BFV ADP 0.007715 0.42004 3.54331
25 1EM6 NBG 0.01527 0.40169 3.54331
26 3IT7 TLA 0.03799 0.40011 3.84615
27 1P4V GLY 0.02391 0.40932 4.33071
28 2HQM FAD 0.01592 0.40091 4.33071
29 3GGF GVD 0.0162 0.40085 4.33071
30 4V03 ADP 0.002418 0.43974 4.66926
31 1MO9 KPC 0.03953 0.40377 4.72441
32 2Q4X HMH 0.02329 0.41325 4.97738
33 4E1Z 0MX 0.002785 0.41429 5.11811
34 4IDT T28 0.01329 0.40138 5.11811
35 4RZ3 ADP 0.003955 0.42175 5.51181
36 3Q3H UDP 0.01806 0.41435 5.51181
37 4ISS TAR 0.02813 0.40528 5.51181
38 3WLV AZA 0.02726 0.405 5.51181
39 1VHZ APR 0.0146 0.41956 5.55556
40 4WNP 3RJ 0.01049 0.41359 5.90551
41 3LAD FAD 0.01126 0.40752 5.90551
42 3F8D FAD 0.01516 0.41933 6.29921
43 5AX9 4KT 0.008553 0.41021 6.29921
44 2UYQ SAM 0.02436 0.40808 6.29921
45 3AB4 THR 0.02008 0.40769 6.29921
46 1WD4 AHR 0.02438 0.4034 6.29921
47 5HBN RPI 0.01682 0.4116 6.41026
48 5HX8 66P 0.002228 0.4055 6.69291
49 2Z7R STU 0.006653 0.40165 7.08661
50 2OG2 MLI 0.008155 0.4194 7.48031
51 5NE2 DGL 0.01704 0.41383 7.48031
52 1IZO PAM 0.02552 0.40238 7.48031
53 4NAE 1GP 0.03239 0.40002 7.55556
54 2IZ1 ATR 0.007925 0.43125 7.87402
55 1SJN DUP 0.01093 0.40188 8.23529
56 1FL2 FAD 0.003466 0.4269 8.66142
57 2FN1 SAL 0.01732 0.41097 9.05512
58 3I6B KDO 0.02638 0.40574 9.44444
59 3Q9T FAY 0.004163 0.42241 9.44882
60 4GYI ADP 0.006907 0.42235 9.44882
61 2G50 ALA 0.02369 0.40938 9.44882
62 4EUU BX7 0.004653 0.4052 9.44882
63 2PHR MAN MAN BMA MAN 0.01257 0.41803 9.52381
64 2PHF MAN MAN BMA MAN 0.01384 0.41591 9.52381
65 2PHW MAN MAN MAN BMA MAN MAN MAN 0.01751 0.40666 9.52381
66 2PHF MAN MAN 0.02547 0.40655 9.52381
67 2AUY NAG MAN MMA 0.01603 0.4047 9.52381
68 2PHT MAN MAN MAN BMA MAN 0.01955 0.40428 9.52381
69 5UIU 8CG 0.005699 0.40586 10.2362
70 5C2N NAG 0.03445 0.40133 10.4167
71 4MGA 27L 0.01872 0.4181 10.6299
72 5TCI MLI 0.02181 0.40276 11.811
73 1WQ1 AF3 0.02276 0.406 13.253
74 4YNU FAD 0.01411 0.40495 13.3858
75 4YNU LGC 0.01711 0.40447 13.3858
76 4PU6 ASP 0.01992 0.41214 13.7405
77 5I7A 68Q 0.008066 0.4012 14.1104
78 2CHT TSA 0.0235 0.40838 14.9606
79 3EZ2 ADP 0.005081 0.43795 18.5039
80 4J56 FAD 0.01794 0.40033 23.6842
Pocket No.: 2; Query (leader) PDB : 2PHN; Ligand: GDP; 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: 2phn.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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