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: 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
Ligand no: 2; Ligand: GPX; Similar ligands found: 85
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 GNP 0.539216 0.922078
12 0O2 0.537736 0.959459
13 GH3 0.533981 0.946667
14 P2G 0.53125 0.932432
15 G 0.53125 0.933333
16 5GP 0.53125 0.933333
17 G1R 0.529412 0.934211
18 GCP 0.529412 0.922078
19 GAV 0.528846 0.910256
20 GSP 0.524272 0.898734
21 P1G 0.520408 0.92
22 Y9Z 0.518182 0.855422
23 DGT 0.514563 0.922078
24 G2R 0.514019 0.910256
25 G2P 0.509615 0.910256
26 GMV 0.504854 0.922078
27 BGO 0.495798 0.898734
28 GPG 0.495413 0.910256
29 GDP MG 0.495146 0.873418
30 3GP 0.494845 0.92
31 2GP 0.494845 0.959459
32 GKE 0.491071 0.910256
33 GDC 0.491071 0.910256
34 GDD 0.491071 0.910256
35 GDP BEF 0.490385 0.851852
36 ALF 5GP 0.490385 0.841463
37 GP2 0.490196 0.910256
38 GTG 0.486726 0.8875
39 6CK 0.482456 0.8875
40 GMP 0.478261 0.828947
41 G5P 0.478261 0.922078
42 GDP ALF 0.477064 0.841463
43 GTP MG 0.476636 0.873418
44 BEF GDP 0.476636 0.841463
45 GDR 0.473684 0.910256
46 GFB 0.473684 0.910256
47 GCP G 0.472222 0.884615
48 G3A 0.469565 0.922078
49 GDP AF3 0.463636 0.841463
50 GKD 0.461538 0.910256
51 JB2 0.461538 0.910256
52 DG 0.46 0.909091
53 DGP 0.46 0.909091
54 GDX 0.457627 0.922078
55 GPD 0.457627 0.876543
56 YGP 0.45614 0.853659
57 GGZ 0.453704 0.804878
58 35G 0.451923 0.906667
59 PCG 0.451923 0.906667
60 C2E 0.451923 0.894737
61 G G 0.451327 0.884615
62 NGD 0.447154 0.910256
63 U2G 0.447154 0.8875
64 FEG 0.447154 0.833333
65 GDP 7MG 0.440678 0.8625
66 CG2 0.44 0.8875
67 JB3 0.439024 0.898734
68 2MD 0.436508 0.845238
69 GGM 0.436508 0.876543
70 ZGP 0.432 0.823529
71 G1G 0.430769 0.876543
72 TPG 0.428571 0.797753
73 CAG 0.426357 0.835294
74 G G U 0.425 0.909091
75 MD1 0.424242 0.845238
76 5GP 5GP 0.420561 0.857143
77 DG DG 0.417391 0.841463
78 GPC 0.415385 0.833333
79 MGD 0.415385 0.845238
80 PGD 0.413534 0.876543
81 1YC 0.408333 0.918919
82 DBG 0.407407 0.898734
83 G C 0.403101 0.851852
84 IDP 0.401869 0.92
85 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: 12
This union binding pocket(no: 1) in the query (biounit: 1vj7.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2INV FRU FRU 0.005375 0.40914 2.03562
2 1UU6 BGC BGC BGC BGC 0.0233 0.41142 3.125
3 2X34 UQ8 0.04542 0.4141 3.31492
4 2X32 OTP 0.03998 0.41722 3.35196
5 2YG2 FLC 0.01127 0.42802 3.48837
6 2YG2 S1P 0.01162 0.41937 3.48837
7 1ZHX HC3 0.02754 0.40759 3.56234
8 4OMJ 2TX 0.04522 0.40323 3.59712
9 4NJH 2K8 0.03358 0.40916 3.91304
10 1EWJ BLM 0.02266 0.41719 4.7619
11 2AGC DAO 0.01306 0.40202 4.93827
12 5LDQ NAP 0.01299 0.40697 7.34463
Pocket No.: 2; Query (leader) PDB : 1VJ7; Ligand: GDP; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 1vj7.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U08 PLP 0.008967 0.41449 1.81347
2 1ZB6 GST 0.02792 0.41124 3.25733
3 3RGA LSB 0.01197 0.41561 10.9541
4 1U0A BGC BGC BGC BGC 0.01453 0.41057 11.6822
5 3HQR OGA 0.01139 0.41084 12.6016
Pocket No.: 3; Query (leader) PDB : 1VJ7; Ligand: GPX; Similar sites found: 87
This union binding pocket(no: 3) in the query (biounit: 1vj7.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2RKN LP3 0.001673 0.45773 None
2 3WGC PLG 0.003224 0.43027 0.879765
3 1U7T TDT 0.03527 0.41248 1.14943
4 5XDT ZI7 0.04976 0.40007 1.2987
5 4PTZ FMN 0.01693 0.40884 1.52672
6 3PE6 ZYH 0.00605 0.43354 1.65016
7 2XIQ MLC 0.02335 0.41258 1.78117
8 4C2C ALA VAL PRO ALA 0.01268 0.41102 1.78117
9 1YOA FAD 0.02711 0.40677 1.88679
10 4LTN NAI 0.01203 0.42885 2.03046
11 4LTN FMN 0.01052 0.42885 2.03046
12 1ZDT PEF 0.003246 0.45587 2.07469
13 1HXD BTN 0.004986 0.44223 2.18069
14 3P9C SAH 0.03489 0.40324 2.1978
15 3I51 45C 0.008037 0.41612 2.22222
16 1XAJ CRB 0.01657 0.42998 2.25989
17 1XAJ NAD 0.01835 0.42998 2.25989
18 1TLL FAD 0.02224 0.40293 2.29008
19 3EUT DCR 0.02968 0.40819 2.37467
20 4JD0 1KH 0.007454 0.40385 2.39044
21 2BLE 5GP 0.01601 0.41465 2.45232
22 2O7B HC4 0.02849 0.40008 2.54453
23 4FK7 P34 0.00234 0.42265 2.62009
24 4LNL PLG 0.002324 0.43475 2.7027
25 4LNL 2BO 0.003031 0.43125 2.7027
26 3PXP MYR 0.01214 0.42179 2.73973
27 1OJ7 NZQ 0.03099 0.4195 2.79898
28 3UBM COA 0.02727 0.41268 2.79898
29 1GZF NAD 0.006904 0.42752 2.8436
30 3A5Y KAA 0.02218 0.41566 2.89855
31 3A5Z KAA 0.0247 0.41272 3.04878
32 1CZA GLC 0.005236 0.42704 3.05344
33 1MDB AMP DBH 0.02708 0.40033 3.05344
34 3E7O 35F 0.02446 0.40564 3.05556
35 1YUC EPH 0.02546 0.40198 3.13725
36 2VHW NAI 0.04395 0.40069 3.18302
37 1VPV PLM 0.02859 0.40663 3.33333
38 3F6R FMN 0.01768 0.40123 3.37838
39 4BKJ STI 0.03139 0.40264 3.49206
40 5N2I NAP 0.02241 0.40501 3.87931
41 2CJW GDP 0.01333 0.40191 4.16667
42 4D3F NAP 0.01787 0.41213 4.19355
43 1REQ DCA 0.02018 0.42679 4.3257
44 2HK9 NAP 0.03042 0.41043 4.36364
45 1OKC CXT 0.006907 0.43533 4.3771
46 1UNB PN1 0.01996 0.4187 4.50161
47 2XVM SAH 0.01032 0.40878 4.52261
48 3EYA TDP 0.0004914 0.50027 4.58015
49 4FXQ G9L 0.001388 0.44516 4.58015
50 4DHY GLC 0.01028 0.43093 4.58015
51 3O8M GLC 0.006463 0.41384 4.58015
52 5DQ8 FLF 0.008092 0.4363 4.58333
53 2HT6 GDP 0.01561 0.40134 4.5977
54 4UBS DIF 0.005429 0.41294 5.08906
55 2QUN FUD 0.01687 0.40288 5.51724
56 4Z3X 4KX 0.0443 0.42777 5.58659
57 4Z3X MTE 0.04251 0.42777 5.58659
58 1N62 MCN 0.048 0.40312 5.59796
59 1JXZ BCA 0.02048 0.41127 5.94796
60 1NZY BCA 0.02179 0.41017 5.94796
61 1MDC PLM 0.004224 0.44645 6.06061
62 2C1X UDP 0.01928 0.41004 6.87023
63 2A9K NAD 0.003447 0.45552 6.95187
64 4GOX A3P 0.005907 0.43867 7.02875
65 1S4M LUM 0.01123 0.41748 7.16724
66 3MDV CL6 0.003667 0.47276 7.67544
67 3OID TCL 0.01136 0.40926 7.75194
68 3A0T ADP 0.02474 0.40059 7.89474
69 5EWK P34 0.001594 0.40767 8
70 2YFB SIN 0.002023 0.4049 8.13953
71 1GOT GDP 0.03147 0.4025 8.21918
72 2PS1 PRP 0.02523 0.40596 8.84956
73 4ZKD GDP 0.02055 0.42154 8.90585
74 2YAJ 4HP 0.01239 0.40502 9.30233
75 4DQ2 BTX 0.007826 0.44713 9.45122
76 3ZL8 ADP 0.01963 0.41135 9.92366
77 3ZOD HQE 0.02665 0.40317 9.94764
78 1DL5 SAH 0.01737 0.41797 10.0946
79 3I54 CMP 0.02033 0.40293 10.4418
80 3CEV ARG 0.01754 0.40174 10.7023
81 2XGT NSS 0.0278 0.40042 11.9593
82 1JS3 PLP 142 0.006551 0.42647 12.2137
83 1ELR ACE MET GLU GLU VAL ASP 0.0168 0.4098 13.7405
84 1T5B FMN 0.01687 0.4006 15.4229
85 4Q9M 2ZW 0.01043 0.42515 15.4472
86 4Q9M FPP 0.01911 0.42515 15.4472
87 3EFS BTN 0.008375 0.43092 18.8841
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