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Receptor
PDB id Resolution Class Description Source Keywords
1VJ7 2.1 Å EC: 3.1.7.2 CRYSTAL STRUCTURE OF THE BIFUNCTIONAL CATALYTIC FRAGMENT OF THE RELA/SPOT HOMOLOG FROM STREPTOCOCCUS EQUISIMILIS. STREPTOCOCCUS DYSGALACTIAE SUBSP. EQUIORGANISM_TAXID: 119602 HD DOMAIN ALPHA BETA 2-LAYER SANDWICH HELIX BUNDLE MANGANPPG2-prime :3-prime P (P)PPGPP PPGPP RELA SPOT STRINGENT RESPONSESTRINGENT FACTOR STRINGENT EFFECTOR MAGIC SPOT RSH HYDRTRANSFERASE
Ref.: CONFORMATIONAL ANTAGONISM BETWEEN OPPOSING ACTIVE S BIFUNCTIONAL RELA/SPOT HOMOLOG MODULATES (P)PPGPP M DURING THE STRINGENT RESPONSE. CELL(CAMBRIDGE,MASS.) V. 117 57 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:998;
B:1998;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
GPX B:1999;
Valid;
none;
submit data
505.165 C10 H14 N5 O13 P3 c1nc2...
MN A:997;
B:1997;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VJ7 2.1 Å EC: 3.1.7.2 CRYSTAL STRUCTURE OF THE BIFUNCTIONAL CATALYTIC FRAGMENT OF THE RELA/SPOT HOMOLOG FROM STREPTOCOCCUS EQUISIMILIS. STREPTOCOCCUS DYSGALACTIAE SUBSP. EQUIORGANISM_TAXID: 119602 HD DOMAIN ALPHA BETA 2-LAYER SANDWICH HELIX BUNDLE MANGANPPG2-prime :3-prime P (P)PPGPP PPGPP RELA SPOT STRINGENT RESPONSESTRINGENT FACTOR STRINGENT EFFECTOR MAGIC SPOT RSH HYDRTRANSFERASE
Ref.: CONFORMATIONAL ANTAGONISM BETWEEN OPPOSING ACTIVE S BIFUNCTIONAL RELA/SPOT HOMOLOG MODULATES (P)PPGPP M DURING THE STRINGENT RESPONSE. CELL(CAMBRIDGE,MASS.) V. 117 57 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1VJ7 - GPX C10 H14 N5 O13 P3 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 1 families.
1 1VJ7 - GPX C10 H14 N5 O13 P3 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 1 families.
1 1VJ7 - GPX C10 H14 N5 O13 P3 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
Ligand no: 2; Ligand: GPX; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 GPX 1 1
2 GDP 0.634409 0.946667
3 UCG 0.632479 0.910256
4 G3D 0.602041 0.959459
5 G4P 0.59 0.959459
6 GTP 0.581633 0.946667
7 DGI 0.56701 0.922078
8 SGP 0.56383 0.871795
9 GP3 0.556701 0.922078
10 GNH 0.545455 0.934211
11 9GM 0.539216 0.922078
12 GNP 0.539216 0.922078
13 0O2 0.537736 0.959459
14 GH3 0.533981 0.946667
15 G 0.53125 0.933333
16 P2G 0.53125 0.932432
17 5GP 0.53125 0.933333
18 G1R 0.529412 0.934211
19 GCP 0.529412 0.922078
20 GAV 0.528846 0.910256
21 GSP 0.524272 0.898734
22 P1G 0.520408 0.92
23 Y9Z 0.518182 0.855422
24 DGT 0.514563 0.922078
25 G2R 0.514019 0.910256
26 G2P 0.509615 0.910256
27 GMV 0.504854 0.922078
28 BGO 0.495798 0.898734
29 GPG 0.495413 0.910256
30 2GP 0.494845 0.959459
31 3GP 0.494845 0.92
32 GDC 0.491071 0.910256
33 GKE 0.491071 0.910256
34 GDD 0.491071 0.910256
35 ALF 5GP 0.490385 0.841463
36 GP2 0.490196 0.910256
37 GTG 0.486726 0.8875
38 6CK 0.482456 0.8875
39 G5P 0.478261 0.922078
40 GMP 0.478261 0.828947
41 ALF GDP 0.477064 0.841463
42 GDP ALF 0.477064 0.841463
43 GDR 0.473684 0.910256
44 GFB 0.473684 0.910256
45 G3A 0.469565 0.922078
46 GDP AF3 0.463636 0.841463
47 JB2 0.461538 0.910256
48 GKD 0.461538 0.910256
49 DGP 0.46 0.909091
50 DG 0.46 0.909091
51 GPD 0.457627 0.876543
52 GDX 0.457627 0.922078
53 YGP 0.45614 0.853659
54 GGZ 0.453704 0.804878
55 C2E 0.451923 0.894737
56 35G 0.451923 0.906667
57 PCG 0.451923 0.906667
58 GCP G 0.451327 0.894737
59 U2G 0.447154 0.8875
60 NGD 0.447154 0.910256
61 FEG 0.447154 0.833333
62 GDP 7MG 0.440678 0.8625
63 CG2 0.44 0.8875
64 JB3 0.439024 0.898734
65 GGM 0.436508 0.876543
66 2MD 0.436508 0.845238
67 G G 0.435897 0.897436
68 ZGP 0.432 0.823529
69 G1G 0.430769 0.876543
70 TPG 0.428571 0.797753
71 CAG 0.426357 0.835294
72 MD1 0.424242 0.845238
73 5GP 5GP 0.420561 0.857143
74 DG DG 0.417391 0.841463
75 GPC 0.415385 0.833333
76 MGD 0.415385 0.845238
77 PGD 0.413534 0.876543
78 G U 0.409449 0.851852
79 1YC 0.408333 0.918919
80 DBG 0.407407 0.898734
81 G C 0.403101 0.851852
82 IDP 0.401869 0.92
83 AKW 0.401575 0.843373
84 G A A A 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VJ7; Ligand: GDP; Similar sites found with APoc: 29
This union binding pocket(no: 1) in the query (biounit: 1vj7.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2WA4 069 2.00573
2 2INV FRU FRU 2.03562
3 2IGA XX2 2.46575
4 4UIB GWX 2.60586
5 4AML GYU 2.92398
6 3X01 AMP 3.05344
7 1UU6 BGC BGC BGC BGC 3.125
8 2X34 UQ8 3.31492
9 2X32 OTP 3.35196
10 2YG2 FLC 3.48837
11 2YG2 S1P 3.48837
12 2GMH UQ5 3.56234
13 1ZHX HC3 3.56234
14 4OMJ 2TX 3.59712
15 4NJH SAM 3.91304
16 4NJH 2K8 3.91304
17 5ABX MGP 4.21053
18 5TH5 7C5 4.56274
19 5ZM4 AKG 4.57516
20 1EWJ BLM 4.7619
21 6GW1 CHO 4.77707
22 2AGC DAO 4.93827
23 4WVO 3UZ 5.74018
24 5LDQ NAP 7.34463
25 1LGT BP3 9.76431
26 4LA7 A1O 9.84456
27 2QL9 CIT 11.3402
28 6EWZ GTP 15.6118
29 5UR6 8KM 19.337
Pocket No.: 2; Query (leader) PDB : 1VJ7; Ligand: GDP; Similar sites found with APoc: 15
This union binding pocket(no: 2) in the query (biounit: 1vj7.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1U08 PLP 1.81347
2 5FP3 3JI 2.29008
3 2ZC0 PMP 2.79898
4 1GA8 DEL 2.89389
5 5Z46 8XL 2.91262
6 2ZRU FMN 2.98913
7 6FUL E7Z 3.05344
8 1ZB6 GST 3.25733
9 5L9G MO0 3.7037
10 6FKW PQQ 3.81679
11 5GVL PLG 4.07125
12 5GVL GI8 4.07125
13 3RGA LSB 10.9541
14 1U0A BGC BGC BGC BGC 11.6822
15 3HQR OGA 12.6016
Pocket No.: 3; Query (leader) PDB : 1VJ7; Ligand: GPX; Similar sites found with APoc: 144
This union binding pocket(no: 3) in the query (biounit: 1vj7.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2RKN LP3 None
2 3WGC PLG 0.879765
3 1U7T TDT 1.14943
4 5XDT ZI7 1.2987
5 2QE0 NAP 1.52672
6 4PTZ FMN 1.52672
7 3MKH FAD 1.52672
8 5ZUN 9JX 1.63934
9 2DXU BT5 1.70213
10 1WPY BTN 1.70213
11 2XIQ MLC 1.78117
12 4C2C ALA VAL PRO ALA 1.78117
13 3NKS ACJ 1.78117
14 1YOA FAD 1.88679
15 4UTG ANP 2.02312
16 4LTN FMN 2.03046
17 4LTN NAI 2.03046
18 2YOO K2B 2.03562
19 3E9I XAH 2.03562
20 6F3M ADN 2.03562
21 1ZDT PEF 2.07469
22 1HXD BTN 2.18069
23 3P9C SAH 2.1978
24 3I51 45C 2.22222
25 1TLL FAD 2.29008
26 3EUT DCR 2.37467
27 4JD0 1KH 2.39044
28 2BLE 5GP 2.45232
29 2IGA XX3 2.46575
30 2O7B HC4 2.54453
31 4FK7 P34 2.62009
32 4LNL PLG 2.7027
33 4LNL 2BK 2.7027
34 4LNL 2BO 2.7027
35 3PXP MYR 2.73973
36 1OJ7 NZQ 2.79898
37 2WET FAD 2.79898
38 1GQ2 NAP 2.79898
39 3UBM COA 2.79898
40 4E70 N7I 2.83505
41 1GZF NAD 2.8436
42 3A5Y KAA 2.89855
43 5O4J 9KH 2.91971
44 5O4J SAH 2.91971
45 3A5Z KAA 3.04878
46 1CZA GLC 3.05344
47 1MDB AMP DBH 3.05344
48 3E7O 35F 3.05556
49 3G1Z AMP 3.06748
50 3VVY ET 3.09278
51 1YUC EPH 3.13725
52 2VHW NAI 3.18302
53 4QS9 BGC 3.30789
54 5KOK R9T 3.30789
55 5KOK SAH 3.30789
56 5KOK S9T 3.30789
57 5AEW BNL 3.30789
58 1VPV PLM 3.33333
59 3F6R FMN 3.37838
60 2OM2 GDP 3.38462
61 5DM1 5D7 3.74532
62 4YC0 5OF 3.76569
63 4ITR GDP 3.79747
64 4GA6 AMP 3.81679
65 5N2I NAP 3.87931
66 2CJW GDP 4.16667
67 4D3F NAP 4.19355
68 5X13 HC4 4.25532
69 1REQ DCA 4.3257
70 3AI7 TPP 4.3257
71 2HK9 NAP 4.36364
72 1OKC CXT 4.3771
73 1UNB PN1 4.50161
74 2XVM SAH 4.52261
75 3EYA TDP 4.58015
76 4DHY GLC 4.58015
77 3O8M BGC 4.58015
78 3O8M GLC 4.58015
79 5YB7 FAD 4.58015
80 5YB7 ORN 4.58015
81 4FXQ G9L 4.58015
82 5DQ8 FLF 4.58333
83 2HT6 GDP 4.5977
84 2A8Y MTA 4.81482
85 4WMY 3S6 5.08906
86 5WS9 AMP 5.08906
87 4UBS DIF 5.08906
88 4BG4 ADP 5.33708
89 5W7R 9Z7 5.34351
90 6FYL 3NG 5.50964
91 2QUN FUD 5.51724
92 4Z3X 4KX 5.58659
93 4Z3X MTE 5.58659
94 4XRZ SI6 5.59796
95 1N62 MCN 5.59796
96 2PYY GLU 5.70175
97 4XTX 590 5.92593
98 1JXZ BCA 5.94796
99 1NZY BCA 5.94796
100 2XD9 XD9 5.98802
101 1MDC PLM 6.06061
102 3LDW ZOL 6.10687
103 5C2H 4XU 6.62983
104 6AP6 TLF 6.69145
105 2C1X UDP 6.87023
106 4YRY NAD 6.88406
107 2A9K NAD 6.95187
108 4GOX A3P 7.02875
109 1CM0 COA 7.14286
110 1S4M LUM 7.16724
111 3OQJ 3CX 7.393
112 3MDV CL6 7.67544
113 3OID TCL 7.75194
114 4DI8 0GZ 7.92079
115 4DI8 0GY 7.92079
116 5EWK P34 8
117 2YFB SIN 8.13953
118 1GOT GDP 8.21918
119 6D6L FY4 8.82353
120 2PS1 PRP 8.84956
121 4ZKD GDP 8.90585
122 2YAJ 4HP 9.30233
123 4DQ2 BTX 9.45122
124 3ZL8 ADP 9.92366
125 3ZOD HQE 9.94764
126 3ZOD FMN 9.94764
127 1DL5 SAH 10.0946
128 3I54 CMP 10.4418
129 3CEV ARG 10.7023
130 5Z84 PGV 10.9589
131 5ZCO PGV 10.9589
132 3ZLR X0B 11.3924
133 2XGT NSS 11.9593
134 1JS3 PLP 142 12.2137
135 1ELR ACE MET GLU GLU VAL ASP 13.7405
136 5ZJ5 NAI 14.1975
137 2UXI G50 15.2381
138 1T5B FMN 15.4229
139 4Q9M FPP 15.4472
140 4Q9M 2ZW 15.4472
141 3D36 ADP 17.3913
142 3EFS BTN 18.8841
143 4R3U 3HC 18.9873
144 4R3U 3KK 18.9873
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