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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 36 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 24 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 19 families.
1 2PHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 161
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 9GM 0.839506 0.973684
6 GNP 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PHN; Ligand: GDP; Similar sites found with APoc: 196
This union binding pocket(no: 1) in the query (biounit: 2phn.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4OVZ P85 None
2 4X9D U5P None
3 6CS9 PIO None
4 4WXJ GLU None
5 4OW0 S88 None
6 1PTR PRB None
7 1RTW MP5 None
8 1BYG STU 1.1811
9 4Z4P SAH 1.20482
10 3PN1 IVH 1.5748
11 1H74 ILE 1.5748
12 2P3V SRT 2.3622
13 5GUD 2IT 2.3622
14 5GUD NDP 2.3622
15 4BHN BH9 2.3622
16 3Q9L ATP 2.3622
17 2BHZ MAL 2.3622
18 3PTG 932 2.3622
19 2Y65 ADP 2.3622
20 4AGS GSH 2.3622
21 1O5Q PYR 2.3622
22 4MRP GSH 2.3622
23 5J1J ANP 2.3622
24 3TKI S25 2.3622
25 1GZ4 ATP 2.3622
26 1ION ADP 2.46914
27 1G3Q ADP 2.53165
28 2C5S AMP 2.75591
29 4NZ6 DLY 2.75591
30 1T9D 1MM 2.75591
31 1T9D FAD 2.75591
32 1T9D PYD 2.75591
33 1T9D P25 2.75591
34 3B8I OXL 2.75591
35 4F9C 0SX 2.77778
36 5N49 8LW 2.96296
37 2ZL4 ALA ALA ALA ALA 3.06122
38 2ZV2 609 3.14961
39 2J5S KTA 3.14961
40 4OH4 ANP 3.14961
41 3UIM ANP 3.14961
42 2WE0 UMP 3.14961
43 1GPM AMP 3.14961
44 2WPF WPF 3.14961
45 2NUN ADP 3.14961
46 1BZL FAD 3.14961
47 2WPF FAD 3.14961
48 4MIG G3F 3.14961
49 5TPC GAL SIA NGA GAL SIA 3.14961
50 5A96 GTP 3.21285
51 6BFN DL1 3.54331
52 3BFV ADP 3.54331
53 5D63 FUC GLA GLA 3.54331
54 3KVY R2B 3.54331
55 3HQ9 OXL 3.54331
56 6F5W KG1 3.54331
57 3B4Y F42 3.54331
58 4M3P HCS 3.54331
59 3HWW AKG 3.54331
60 4CP8 MLI 3.54331
61 3JQM GTP 3.82166
62 3IT7 TLA 3.84615
63 5C9P FUC 3.93701
64 4WBD CIT 3.93701
65 4UBS DIF 3.93701
66 3ORQ ADP 3.93701
67 1GET NAP 3.93701
68 1GET FAD 3.93701
69 1JG9 GLC 3.93701
70 2H8H H8H 3.93701
71 2C3H GLC GLC 4.08163
72 5YZ2 AMP 4.16667
73 1CT9 AMP 4.33071
74 1CT9 GLN 4.33071
75 3DLS ADP 4.33071
76 2HQM FAD 4.33071
77 3GGF GVD 4.33071
78 1H5R THM 4.33071
79 6FXR UDP 4.33071
80 2H6B 3C4 4.4
81 4V03 ADP 4.66926
82 4WZ6 ATP 4.72441
83 1MO9 KPC 4.72441
84 1GQ2 NAP 4.72441
85 1MO9 FAD 4.72441
86 2POC UD1 4.90463
87 2Q4X HMH 4.97738
88 1GPE FAD 5.11811
89 6CI9 F3V 5.11811
90 5OC1 FAD 5.11811
91 2Z49 AMG 5.11811
92 3LXN MI1 5.11811
93 4UX9 ANP 5.11811
94 3NYC FAD 5.11811
95 3NYC IAR 5.11811
96 4E1Z 0MX 5.11811
97 4IDT T28 5.11811
98 2HJ4 PNZ 5.11811
99 2Z48 NGA 5.11811
100 3EFS ATP 5.15021
101 3KIH GDL 5.15464
102 1U70 MTX 5.37634
103 1U70 NDP 5.37634
104 5X7Q GLC GLC 5.51181
105 4YKG FAD 5.51181
106 4RZ3 ADP 5.51181
107 3Q3H UDP 5.51181
108 4ISS TAR 5.51181
109 3WLV AZA 5.51181
110 1VHZ APR 5.55556
111 1UA4 AMP 5.71429
112 4WNP 3RJ 5.90551
113 4FBL SPD 5.90551
114 3LAD FAD 5.90551
115 1YP4 ADP 5.90551
116 2G7C GLA GAL NAG 5.90551
117 2WD7 VGD 5.90551
118 4Y4V DAL 5.90551
119 5YRV 5AD 6
120 3W6G FLC 6.01852
121 2UXR ICT 6.29921
122 3F8D FAD 6.29921
123 5AX9 4KT 6.29921
124 3AB4 THR 6.29921
125 2UYQ SAM 6.29921
126 1WD4 AHR 6.29921
127 4Z24 FAD 6.29921
128 4E03 ADP 6.31068
129 5LMK 6ZK 6.69291
130 5O0J 8BR 6.69291
131 5WO4 B7V 6.69291
132 6C7Y ADP 6.69291
133 3GD8 GOL 6.72646
134 4NTO 1PW 6.76329
135 4GYS MLI 7.08661
136 2AOU CQA 7.08661
137 2Z7R STU 7.08661
138 2OG2 MLI 7.48031
139 5NE2 DGL 7.48031
140 5XWC NAP 7.48031
141 5XWC 2IT 7.48031
142 5XWC 8GL 7.48031
143 3KJI ADP 7.48031
144 2NU8 COA 7.48031
145 1IZO PAM 7.48031
146 4NAE 1GP 7.55556
147 2IZ1 ATR 7.87402
148 1YQT ADP 7.87402
149 1V59 NAD 7.87402
150 1SJN DUP 8.23529
151 2ZZV LAC 8.26772
152 1FL2 FAD 8.66142
153 1T3Q MCN 8.66142
154 2X7I CIT 8.66142
155 4LFL TG6 8.72093
156 2FN1 SAL 9.05512
157 3I6B KDO 9.44444
158 3Q9T FAY 9.44882
159 4GYI ADP 9.44882
160 5WS9 AMP 9.44882
161 2G50 ALA 9.44882
162 4EUU BX7 9.44882
163 2PHU MAN MAN 9.52381
164 2PHR MAN MAN BMA MAN 9.52381
165 2PHF MAN MAN BMA MAN 9.52381
166 2PHU MAN MAN MAN BMA MAN 9.52381
167 2PHW MAN MAN MAN BMA MAN MAN MAN 9.52381
168 2PHF MAN MAN 9.52381
169 1Q8P MAN MMA 9.52381
170 2AUY NAG MAN MMA 9.52381
171 2PHT MAN MAN MAN BMA MAN 9.52381
172 2A8X FAD 9.84252
173 2VAR AMP 10.2362
174 5UIU 8CG 10.2362
175 3SBZ MLI 10.3175
176 5C2N NAG 10.4167
177 4MGA 27L 10.6299
178 2OEM 1AE 10.6299
179 3FWY ADP 10.828
180 2O66 FLC 11.1111
181 3AXM 6PG 11.6279
182 5VZ0 ADP 11.811
183 5ODQ 9SB 11.811
184 5TCI MLI 11.811
185 5DEX GLY 12.2047
186 2ZUX RAM 12.5984
187 3QDK QDK 12.9921
188 1WQ1 AF3 13.253
189 4YNU FAD 13.3858
190 4YNU LGC 13.3858
191 4PU6 ASP 13.7405
192 2CHT TSA 14.9606
193 1VAY AZA 16.9291
194 3EZ2 ADP 18.5039
195 4J56 FAD 23.6842
196 1ONI BEZ 31.1594
Pocket No.: 2; Query (leader) PDB : 2PHN; Ligand: GDP; Similar sites found with APoc: 59
This union binding pocket(no: 2) in the query (biounit: 2phn.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 2V58 LZJ 1.9685
3 5H4S RAM 1.9685
4 3UEC ALA ARG TPO LYS 2.05479
5 2VGD XYP XYP 2.29358
6 4QS9 BGC 2.3622
7 4CS9 AMP 2.6455
8 2GZ3 NAP 2.75591
9 5Z21 OXM 2.75591
10 5YSQ INS 3.14961
11 6APL C5P 3.14961
12 1COY FAD 3.14961
13 1LDN FBP 3.14961
14 3A76 SPD 3.40909
15 3B9Q MLI 3.54331
16 1RYD GLC 3.54331
17 1O5O U5P 3.61991
18 3B6C SDN 3.84615
19 1LK7 DER 3.93013
20 5C03 AGS 3.93701
21 2OUA AES 4.78723
22 2XYA 7L4 4.94506
23 3QVP FAD 5.11811
24 3LXK MI1 5.11811
25 1O8B ABF 5.47945
26 3DUV KDO 5.51181
27 3KIF GDL 5.66038
28 4HNN LYS 6.29921
29 2B3B GLC 6.69291
30 5IUY BOG 6.69291
31 2B3B BGC 6.69291
32 2J9L ATP 7.02703
33 4HZO COA 7.48031
34 6FUL PG0 7.87402
35 5AWM ANP 7.87402
36 5A1S FLC 7.87402
37 4UP5 94W 8.08081
38 3K6V CIT 8.19209
39 4OKD GLC GLC GLC 8.26772
40 5N9X THR 8.26772
41 5F1V 3VN 8.66142
42 3GLC R5P 8.66142
43 2V2G BEZ 9.01288
44 4IA6 EIC 9.44882
45 5HVJ ANP 9.44882
46 2PHR MAN MAN 9.52381
47 2PHW MAN MAN 9.52381
48 1Q8V MAN MAN 9.52381
49 2GND MAN MMA 9.52381
50 1UKG MMA 9.52381
51 2GND MAN 9.52381
52 1Q8S MAN MMA 9.52381
53 1Q8O MAN MMA 9.52381
54 3KPB SAM 9.83607
55 3AYI HCI 9.84252
56 3AYI FAD 9.84252
57 5Y5Q DUT 10.9195
58 3ALN ANP 11.4173
59 1WRA PC 11.4173
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