Receptor
PDB id Resolution Class Description Source Keywords
5UFQ 2.2 Å EC: 7.-.-.- K-RASG12D(GNP)/R11.1.6 COMPLEX HOMO SAPIENS RAS GTPASE COMPLEX INHIBITOR HYDROLASE-DE NOVO PROTEIN C
Ref.: AN ENGINEERED PROTEIN ANTAGONIST OF K-RAS/B-RAF INT SCI REP V. 7 5831 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNP A:201;
B:201;
Valid;
Valid;
none;
none;
submit data
522.196 C10 H17 N6 O13 P3 c1nc2...
CA A:205;
B:204;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
CD A:206;
B:205;
Invalid;
Invalid;
none;
none;
submit data
112.411 Cd [Cd+2...
CL A:204;
A:203;
B:203;
D:101;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
MG B:202;
A:202;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5O2T 2.19 Å EC: 7.-.-.- HUMAN KRAS IN COMPLEX WITH DARPIN K27 HOMO SAPIENS KRAS RAS SIGNALLING DARPIN NUCLEOTIDE EXCHANGE SIGNALING
Ref.: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A DAR INHIBITS RAS NUCLEOTIDE EXCHANGE. NAT COMMUN V. 8 16111 2017
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
2 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
3 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
10 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
2 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
3 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
4 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
5 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
6 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
10 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
11 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
14 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
16 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
17 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
19 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
21 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
22 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
23 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
24 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
25 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
26 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
27 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
28 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
30 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
32 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
33 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
34 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 3QBT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 5WFO - 5UU C19 H16 Cl F N2 c1cc(ccc1N....
3 6FA3 Kd = 0.038 uM D1Z C30 H36 N4 O5 CN(C)Cc1cc....
4 5WFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
5 5O2T Kd = 3.9 nM GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
6 5WPM - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
7 5WFR - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
8 5UFQ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
9 6AMB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
10 6FA1 - D2Z C20 H25 N2 O4 C[NH+](C)C....
11 5UFE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
12 5WFP - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
13 5WHB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5WPL - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
15 5XCO - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 1NVU - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 5WHE - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
18 3KUC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
19 1C1Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
20 5TAR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 4DXA - GSP C10 H16 N5 O13 P3 S c1nc2c(n1[....
22 4HDO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
23 3MJH - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 5E95 Kd = 15.7 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 3CF6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
26 2CJW Kd = 2.5 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 6FA4 Kd = 0.051 uM D1W C23 H25 N3 O3 CN(C)Cc1cc....
28 2C5L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
29 4K81 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
30 1LFD - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
31 4KVG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 3TNF - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
33 1ZC4 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
34 1ZC3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
35 2A9K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
36 2A78 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
37 1WQ1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
38 3TKL - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 3DDC - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
40 3KUD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
41 1TU3 - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
42 1UAD Ka = 7260000 M^-1 GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
43 5O74 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
44 3SFV - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4URZ Kd = 3 mM VJP C11 H14 N2 O3 S c1cc(ccc1N....
46 4URX Kd = 1.3 mM HXY C11 H14 Br N c1cc(ccc1C....
47 4URY Kd = 6 mM RV1 C10 H12 N2 O3 S c1cc(ccc1N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GNP; Similar ligands found: 132
No: Ligand ECFP6 Tc MDL keys Tc
1 GNP 1 1
2 9GM 1 1
3 GDP 0.839506 0.973684
4 GP3 0.82716 0.948718
5 GTP 0.809524 0.973684
6 GNH 0.807229 0.986842
7 G1R 0.77907 0.961039
8 GCP 0.77907 0.948718
9 GSP 0.770115 0.925
10 5GP 0.756098 0.960526
11 G 0.756098 0.960526
12 G2R 0.747253 0.936709
13 GMV 0.747126 0.948718
14 GAV 0.714286 0.936709
15 GP2 0.712644 0.936709
16 G2P 0.711111 0.936709
17 Y9Z 0.708333 0.880952
18 GDC 0.690722 0.936709
19 GDD 0.690722 0.936709
20 GKE 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GTG 0.683673 0.91358
24 GDR 0.683673 0.936709
25 GFB 0.683673 0.936709
26 JB2 0.68 0.936709
27 GKD 0.68 0.936709
28 6CK 0.676768 0.91358
29 G3A 0.676768 0.948718
30 GDX 0.673267 0.948718
31 ALF 5GP 0.67033 0.86747
32 YGP 0.663265 0.879518
33 GPD 0.656863 0.902439
34 ALF GDP 0.645833 0.86747
35 GDP AF3 0.645833 0.86747
36 GDP ALF 0.645833 0.86747
37 JB3 0.641509 0.925
38 DBG 0.640351 0.974359
39 G3D 0.638298 0.960526
40 G4P 0.625 0.960526
41 GMP 0.621951 0.857143
42 NGD 0.62037 0.936709
43 GGM 0.618182 0.925926
44 0O2 0.616162 0.960526
45 2MD 0.603604 0.870588
46 CAG 0.60177 0.904762
47 U2G 0.590909 0.91358
48 FEG 0.590909 0.858824
49 GDP 7MG 0.590476 0.888889
50 MGD 0.587719 0.870588
51 G G 0.586538 0.924051
52 ZGP 0.585586 0.848837
53 CG2 0.580357 0.91358
54 ANP 0.568421 0.922078
55 PGD 0.567797 0.902439
56 MD1 0.567797 0.870588
57 3GP 0.56044 0.922078
58 TPG 0.558333 0.822222
59 GH3 0.55 0.948052
60 FE9 0.546219 0.778947
61 GPX 0.539216 0.922078
62 G4M 0.539062 0.860465
63 DGI 0.536082 0.9
64 BGO 0.535088 0.901235
65 IDP 0.53125 0.947368
66 DGT 0.53 0.9
67 2GP 0.526882 0.935065
68 G1R G1R 0.520325 0.901235
69 GCP G 0.518868 0.897436
70 A G 0.516949 0.911392
71 U A G G 0.512605 0.911392
72 G A A A 0.504202 0.9
73 AGO 0.504202 0.91358
74 P2G 0.5 0.860759
75 G1G 0.5 0.902439
76 R7I 0.49505 0.922078
77 MGP 0.49505 0.936709
78 R5I 0.49505 0.922078
79 PGD O 0.492063 0.831461
80 6G0 0.490196 0.936709
81 P1G 0.489796 0.85
82 AKW 0.483051 0.869048
83 DG 0.474227 0.8875
84 DGP 0.474227 0.8875
85 G U 0.466667 0.878049
86 IMP 0.463918 0.934211
87 G2Q 0.462963 0.936709
88 GPC 0.459677 0.858824
89 G C 0.459016 0.878049
90 GTA 0.448276 0.91358
91 G7M 0.444444 0.924051
92 MAP 0.439252 0.898734
93 G G G RPC 0.435484 0.853659
94 B4P 0.434343 0.871795
95 AP5 0.434343 0.871795
96 ADP 0.434343 0.896104
97 A2D 0.43299 0.871795
98 AT4 0.43 0.8625
99 G G G C 0.426357 0.890244
100 AU1 0.425743 0.922078
101 SGP 0.425743 0.807229
102 BA3 0.424242 0.871795
103 A G C C 0.423077 0.888889
104 35G 0.423077 0.909091
105 PCG 0.423077 0.909091
106 C2E 0.423077 0.897436
107 APC G U 0.421875 0.864198
108 HEJ 0.421569 0.896104
109 ATP 0.421569 0.896104
110 ACQ 0.419048 0.873418
111 5GP 5GP 0.419048 0.860759
112 5FA 0.417476 0.896104
113 AQP 0.417476 0.896104
114 01G 0.417391 0.880952
115 AN2 0.415842 0.909091
116 UNP 0.415842 0.810127
117 6AD 0.415094 0.821429
118 M33 0.411765 0.860759
119 ITT 0.411765 0.846154
120 G C C C 0.410448 0.901235
121 HFD 0.409524 0.851852
122 G U34 0.408 0.86747
123 ACP 0.407767 0.873418
124 6YZ 0.407407 0.873418
125 AR6 0.403846 0.871795
126 APR 0.403846 0.871795
127 DG DG 0.403509 0.845238
128 A4P 0.403226 0.848837
129 UCG 0.402985 0.888889
130 SAP 0.4 0.851852
131 AGS 0.4 0.851852
132 AD9 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5O2T; Ligand: GSP; Similar sites found with APoc: 83
This union binding pocket(no: 1) in the query (biounit: 5o2t.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3WY9 GDP 5.32544
2 3U6B GDP 6.95187
3 4P3Y GDP 6.95187
4 2BVN GNP 6.95187
5 3U6K GDP 6.95187
6 1KK1 GNP 7.69231
7 5W75 GDP 8.28402
8 2WJG GDP 8.87574
9 3EC1 GDP 8.87574
10 4RD0 GDP 9.46746
11 5W7Q GDP 10.0592
12 5W76 GDP 10.0592
13 2WIC GNP 10.6509
14 1SKQ GDP 11.2426
15 2C77 GNP 11.8343
16 4J0Q GDP 12.426
17 1FQK ALF 13.9037
18 4TMZ GSP 15.3846
19 4NCN GTP 15.3846
20 4KAX GTP 16.568
21 6G14 G4P 16.568
22 3N5C GDP 17.9012
23 3PCR GTP 17.9012
24 4LC1 GDP 18.9349
25 5CK5 GDP 20.7101
26 2FH5 GTP 24.8521
27 1NRJ GTP 24.8521
28 5FG3 GDP 25.4438
29 1YRB GDP 27.8107
30 5YT0 GDP 28.4024
31 4M9Q GNP 28.4024
32 2A5F GTP 28.9941
33 2J59 GTP 31.9527
34 1RE0 GDP 32.5444
35 5KUT GDP 33.1361
36 2QN6 GDP 33.3333
37 1R4A GNP 33.3333
38 4DCT GDP 33.7278
39 1ZJ6 G3D 33.7278
40 1FQJ ALF 38.0952
41 3A1S GDP 38.4615
42 1FZQ GDP 39.645
43 4ZI2 GNP 39.645
44 4GOJ GNP 39.645
45 5DI3 GNP 41.4201
46 1M7B GTP 44.9704
47 3M1I GTP 46.7456
48 3WYF GTP 46.7456
49 3WYG GTP 46.7456
50 3GJX GTP 47.3373
51 3GJ4 GDP 47.3373
52 3GJ7 GDP 47.3373
53 3GJ5 GDP 47.3373
54 3REF GDP 47.3373
55 1IBR GNP 47.929
56 1GWN GTP 47.929
57 4HAT GNP 47.929
58 1WA5 GTP 47.929
59 3GJ3 GDP 47.929
60 5BXQ GDP 47.929
61 3RAB GNP 47.929
62 3CH5 GDP 47.929
63 2EW1 GNP 48.5207
64 1NF3 GNP 49.1124
65 5XC5 GTP 49.1124
66 4DKX GDP 49.7041
67 5UWJ GNP 49.7041
68 5UWI GNP 49.7041
69 5UWR GNP 49.7041
70 5DI9 GNP 49.7041
71 5LEF GTP 49.7041
72 5UWP GNP 49.7041
73 5UWQ GNP 49.7041
74 5DHF GNP 49.7041
75 5UWS GNP 49.7041
76 6CIT GNP 49.7041
77 5UWO GNP 49.7041
78 5UWT GNP 49.7041
79 5UWW GNP 49.7041
80 5UWU GNP 49.7041
81 5UWH GNP 49.7041
82 5UPK GNP 49.7041
83 2WKQ GTP 49.7041
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