Exploring Binding Site Similarity with CavBase:

Current Achievements and Future Challenges

3rd Joint Sheffield Conference on CheminformaticsApril 21st - 23rd 2004Andreas Bergner, CCDC

Outline

• Introduction (CavBase methods and concept)• Validation work on PLP binding sites• Similarity scoring function• ATP binding sites• Conclusion

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

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

Packing

CavBase and Relibase+

FlatPDBFiles

CoreRelibase

Meta-databases

CavBaseWaterBase

SequenceAlignments

PythonToolkit

ReliscriptGUI

CavBase

CAVITYDATABASE

Cavity DetectionProperty Description

Similarity Search

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).

The pseudo-centre concept

protonation ?

Coding Molecular Recognition into Simple Descriptors

donoracceptor

aliphaticπ/aromatic

NH

O

O

O

N

OO

N

HN

HH

O

NH

Cavity

protein

3D Property Description

Trypsin 1tpo

Similarity Search

Similarity Search

Clique detectionBron-Kerbosch

Similarity Analysis

Scoring based on matching pseudo-centres, and the surface patchesassociated

Similarity Analysis

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

PLP ligand in 1oxo

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

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

“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

A result (1oxo - 1f2d)An example: 1oxo / 1f2d

AcceptorDonor

Don/AccAromaticAliphatic

A result (1oxo - 1f2d)1oxo:Clique pseudo-centres +Matching surface patches

AcceptorDonor

Don/AccAromaticAliphatic

1oxo / 1f2d

AcceptorDonor

Don/AccAromaticAliphatic

1oxo / 1f2dMatching surface areas

AcceptorDonor

Don/AccAromaticAliphatic

1oxo / 1f2dPLP ligands

AcceptorDonor

Don/AccAromaticAliphatic

AcceptorDonor

Don/AccAromaticAliphatic

1oxo / 1f2dPseudo-centres +Binding sites

Problematic Cases

1g76Flavin ligand

1ct5Seleno-methione

Problematic Cases

1em6Glycogen phosphorylaseWater-mediated contacts

Phosphate-binding cupDenesyuk et al., J.Mol.Biol. (2002)

Scoring and Database Searches

PLP (177)Random (385)All (562)

Searching test databasewith PLP cavity (1oxo)

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)

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 =

Similarity Scoring

Standard new

PLPRandomAll

Searching test databasewith PLP cavity (1oxo)

ATP Binding Site Similarity

N1

N3

N6

N7

N

Ribose-phosphate

• Hydrophobic environment aboveand below the ring

• H-bonding partners in adenine ring

C2

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

N1

N3

N6

N7

N

Ribose

Polar neighbours bit stringsextracted using Reliscript

ATP Binding Site Similarity

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

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

ATP Binding Sites

1atn (2.8Å)

1kax (1.7Å)

ATP Binding Site Comparison

1atn/1e4g 1dv2/1csn

Summary

• Identification of binding site similarity• Database search approach• Scoring Function• Versatility of binding sites

Acknowledgements• Stefan Schmitt (AstraZeneca, Mølndal, Sweden)

• Daniel Kuhn (Univ. Marburg, Germany)

• Gerhard Klebe (Univ. Marburg, Germany)

• Robin Taylor (CCDC, Cambridge, UK)

.

A result (1oxo - 1f2d)