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Exploring Binding Site Similarity with CavBase:
Current Achievements and Future Challenges
3rd Joint Sheffield Conference on CheminformaticsApril 21st - 23rd 2004Andreas Bergner, CCDC
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Outline
• Introduction (CavBase methods and concept)• Validation work on PLP binding sites• Similarity scoring function• ATP binding sites• Conclusion
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CavBase
• Database of cavities on protein surfaces• Chemical characterisation of cavities• Similarity searches for non-homologous
proteins, with entire cavities or subpockets
• Developed by S. Schmitt (Univ. Marburg)• Distributed as part of Relibase+ by CCDC
• Idea generator in drug design• Cross reactivity
S.Schmitt et al., J.Mol.Biol. (2002)
A. Weber et al., J.Med.Chem. (2004) COX-2 vs. CA
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Binding Site Similarity Search Methods
• Structural motifso TESS/PROCATo FEATUREo PINTSo ASSAMo …
• Chemical nature of binding siteo CavBaseo eF-Siteo SuMoo …
Catalytic triad
Cofactor binding site
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Packing
CavBase and Relibase+
FlatPDBFiles
CoreRelibase
Meta-databases
CavBaseWaterBase
SequenceAlignments
PythonToolkit
ReliscriptGUI
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CavBase
CAVITYDATABASE
Cavity DetectionProperty Description
Similarity Search
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Cavity Detection
PROTEIN
NO
OO
N
ON
N
O
N
OO
N
N
O
O
N
O
N
N
N
O
Based on the LIGSITE ProgramM.Hendlich et al., J.Mol.Graph. (1997).
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The pseudo-centre concept
protonation ?
Coding Molecular Recognition into Simple Descriptors
donoracceptor
aliphaticπ/aromatic
NH
O
O
O
N
OO
N
HN
HH
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O
NH
Cavity
protein
3D Property Description
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Trypsin 1tpo
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Similarity Search
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Similarity Search
Clique detectionBron-Kerbosch
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Similarity Analysis
Scoring based on matching pseudo-centres, and the surface patchesassociated
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Similarity Analysis
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Validation
• 177 PLP binding proteins• 385 random selection
• 55 standard pharmaceutical target ligand binding sites• 330 completely random
• 562 in total
• PLP binding protein: 27 sequence classes (<30%)• 10 SCOP families
• Find other PLP binding sites• Significance in database search
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PLP ligand in 1oxo
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DOPADecarboxy-
lase
SCOP for PLP Binding Proteins
All-βproteinsα/β proteins
SCOP Root
α/βmultidomain
proteins
FMN-binding
split barrel
F1 ATPaseα/β
subunit-like
Tryptophansynthase
PLP dep.
UDP-GlycosylTransferase/
Phosphorylase
TIMα/β
Barrel
D-amino acidamino-
transferase
D-amino acidamino-
transferase
Alanine-racemase-
like
Tryptophansynthase
PLP dep.
Oligo-saccharide-
phosphorylase
PNP-oxidase-
likeAAT like
Cystathione-synthase-
like
ω-amino acidPyruvateAmino-
transferase
PLP-dependenttransferase
HypotheticalProteinybl036c
FMN-binding
split barrel
Alanine-racemase-
like
Tryptophansynthase
PLP dep.
UDP-GlycosylTransferase/
Phosphorylase
PLP-bindingbarrel
D-amino acidamino-
transferase
PLP-dependenttransferase
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1js3
Initial Classification of Results
All-βproteinsα/β proteins
SCOP Root
α/βmultidomain
proteins
FMN-binding
split barrel
F1 ATPaseα/β
subunit-like
Tryptophansynthase
PLP dep.
UDP-GlycosylTransferase/
Phosphorylase
TIMα/β
Barrel
D-amino acidamino-
transferase
(1ekf)2tod(1sft)1f2d 1em6 1g76Reference:
1oxo
1kmk
1bh9
PLP-dependenttransferase
1ct5
FMN-binding
split barrel
Alanine-racemase-
like
Tryptophansynthase
PLP dep.
UDP-GlycosylTransferase/
Phosphorylase
PLP-bindingbarrel
D-amino acidamino-
transferase
PLP-dependenttransferase
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“Mixed” results
• Phosphate group overlap only• Reasonable global overlap of ligands, but subjectively not convincing
• Subpocket vs. entire cavity search• Results depend on the scoring function (SF1/SF2)• Reasonable results can only be obtained for a subset of the structures in a SCOP family
P P
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A result (1oxo - 1f2d)An example: 1oxo / 1f2d
AcceptorDonor
Don/AccAromaticAliphatic
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A result (1oxo - 1f2d)1oxo:Clique pseudo-centres +Matching surface patches
AcceptorDonor
Don/AccAromaticAliphatic
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1oxo / 1f2d
AcceptorDonor
Don/AccAromaticAliphatic
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1oxo / 1f2dMatching surface areas
AcceptorDonor
Don/AccAromaticAliphatic
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1oxo / 1f2dPLP ligands
AcceptorDonor
Don/AccAromaticAliphatic
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AcceptorDonor
Don/AccAromaticAliphatic
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1oxo / 1f2dPseudo-centres +Binding sites
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Problematic Cases
1g76Flavin ligand
1ct5Seleno-methione
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Problematic Cases
1em6Glycogen phosphorylaseWater-mediated contacts
Phosphate-binding cupDenesyuk et al., J.Mol.Biol. (2002)
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Scoring and Database Searches
PLP (177)Random (385)All (562)
Searching test databasewith PLP cavity (1oxo)
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Standard Scoring
• Similar pseudo-centre distance < 2.1 Å
• Calculate overlap ofsurface points
• Threshold of overlap = 1.0 Å• Local score: 0.0 or 0.7-1.0• Total score = Σ (Local score)
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New Scoring Function• Similar pseudo-centre
distance < 2.1 Å• Find closest distance d between
surface any point P2 in surface patch S2 for each point P1 ofpatch S1
• Calculate score scoreP for each point
• Local score = Σ scoreP• Total score = Σ (Local score)
2.0 for d <= 0.5Å1/d for 0.5 Å < d <= 1.0 Å1/d2 for 1.0 Å < d <= 2.0 Å0.0 for d > 2.0Å
scoreP =
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Similarity Scoring
Standard new
PLPRandomAll
Searching test databasewith PLP cavity (1oxo)
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ATP Binding Site Similarity
N1
N3
N6
N7
N
Ribose-phosphate
• Hydrophobic environment aboveand below the ring
• H-bonding partners in adenine ring
C2
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Capello et al., Proteins (2002)
N1
N3
N6
N7
N
Ribose
H-bond pattern as bit strings
C2
N1 C2 N3 N6t N6c N7
0 1 1 1 1 0
ATP Binding Site Similarity
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N1
N3
N6
N7
N
Ribose
Polar neighbours bit stringsextracted using Reliscript
ATP Binding Site Similarity
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ATP Binding Site Classification
0(30) 0 0 0 0 ADP_600-D_PDB1E79_10 0 0 0 ADP_600-D_PDB1H8H_10 0 0 0 ADP_600-D_PDB1NBM_1...
1(14) 0 0 0 1 ATP_1376_PDB1DEJ_10 0 0 1 ATP_1377-A_PDB1H1V_10 0 0 1 ATP_1478-A_PDB1H4Q_1...
1(3) 0 0 1 0 ATP_606_PDB1HP1_10 0 1 0 ATP_665-A_PDB1HI1_1C0 0 1 0 T5A_214_PDB1MRN_1
1(8) 0 1 0 0 ADP_486_PDB2BUP_10 1 0 0 ATP_486_PDB1KAX_10 1 0 0 ATP_486_PDB1KAY_1...
1(31) 1 0 0 0 128_999_PDB1I5D_11 0 0 0 ADP-ANP_302-A_PDB1E2F_11 0 0 0 ADP-ANP_302-A_PDB1E9C_1...
2(2) 0 1 0 1 ATP_3000_PDB1NSY_10 1 0 1 DND_3000_PDB1EE1_1
2(1) 0 1 1 0 ATP_901-A_PDB1F2U_1
2(2) 1 0 1 0 ATP_2060_PDB1J7K_11 0 1 0 ATP_457_PDB1KYI_1
2(35) 1 1 0 0 ADP-ANP_302-A_PDB1E9B_11 1 0 0 AP5_215-A_PDB1E4Y_11 1 0 0 ATP_1301_PDB1JAG_1...
3(20) 1 1 1 0 A4P_171_PDB1EX8_11 1 1 0 ATP_1000_PDB1DV2_11 1 1 0 ATP_1433-A_PDB1H3E_1...
4(5) 1 1 1 1 ATP_400_PDB1M83_11 1 1 1 ATP_400_PDB1MAU_11 1 1 1 ATP_5501_PDB1MIW_1...
Binding sites: 315PDB entries: 151
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ATP Binding Site Similarity
1 1 1 0 ATP_1001_PDB1DV2_1
0 1 1 0 ATP_381_PDB1FQ1_1
0 1 1 1 ATP_400_PDB1HCK_1
0 1 1 0 ATP_1433-A_PDB1H3E_1
1 1 1 0 ATP_1-F_PDB1FIN_1
1 1 1 0 ATP_5_PDB1KJ8_1
1 1 1 1 ATP_299_PDB1CSN_1
1 1 1 1 ATP_381-B_PDB1QL6_1
1 1 1 0 ATP_1510_PDB1J21_1
1 1 1 0 ATP_1591_PDB1II0_1
0 1 1 0 ATP_1-S_PDB3R1R_1
1 1 1 1 ATP_1500_PDB1B8A_1
1 1 1 1 ATP_802_PDB1A82_1
0 0 0 0 ATP_1_PDB1ATN_1
0 0 0 0 ATP_1-N_PDB2BTF_1
1 0 0 0 ATP_500-T_PDB1E4G_1
1 1 1 1 ATP_486_PDB1KAX_1
0 0 0 0 30 binding sites 1 1 1 0 20 binding sites
• Clustering• Polar vs. apolar cavities
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ATP Binding Sites
1atn (2.8Å)
1kax (1.7Å)
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ATP Binding Site Comparison
1atn/1e4g 1dv2/1csn
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Summary
• Identification of binding site similarity• Database search approach• Scoring Function• Versatility of binding sites
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Acknowledgements• Stefan Schmitt (AstraZeneca, Mølndal, Sweden)
• Daniel Kuhn (Univ. Marburg, Germany)
• Gerhard Klebe (Univ. Marburg, Germany)
• Robin Taylor (CCDC, Cambridge, UK)
.
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A result (1oxo - 1f2d)