FAIRMol

ulfkktlib_3745

Pose ID 7607 Compound 1326 Pose 155

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T12
T. brucei R5P T. brucei
Ligand ulfkktlib_3745
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
88.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.82, H-bond role recall 0.40
Burial
64%
Hydrophobic fit
79%
Reason: strain 88.6 kcal/mol
strain ΔE 88.6 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 64% of hydrophobic surface is solvent-exposed (18/28 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.706 kcal/mol/HA) ✓ Good fit quality (FQ -7.32) ✓ Strong H-bond network (16 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Extreme strain energy (88.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (10) ✗ Many internal clashes (14)
Score
-27.525
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-7.32
FQ (Leeson)
HAC
39
heavy atoms
MW
531
Da
LogP
2.44
cLogP
Strain ΔE
88.6 kcal/mol
SASA buried
64%
Lipo contact
79% BSA apolar/total
SASA unbound
922 Ų
Apolar buried
466 Ų

Interaction summary

HB 16 HY 8 PI 1 CLASH 3 ⚠ Exposure 64%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
64% of hydrophobic surface is solvent-exposed (18/28 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 28 Buried (contacted) 10 Exposed 18 LogP 2.44 H-bonds 16
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (8 atoms exposed)
Final rank2.563Score-27.525
Inter norm-0.747Intra norm0.041
Top1000noExcludedno
Contacts15H-bonds16
Artifact reasongeometry warning; 14 clashes; 10 protein contact clashes; high strain Δ 88.0
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 ARG46 ASP13 CYS72 GLY73 GLY77 HIS14 ILE15 SER74 TYR49

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:CSD72

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap14Native recall0.88
Jaccard0.82RMSD-
HB strict6Strict recall0.50
HB same residue+role4HB role recall0.40
HB same residue5HB residue recall0.50

HB · H-bonds
Mode: permissive. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
155 2.5629984015001437 -0.747059 -27.525 16 15 14 0.88 0.40 - no Current
257 2.7097506770575244 -0.747384 -27.883 4 18 0 0.00 0.00 - no Open
251 4.443560184982545 -0.50084 -17.9358 8 13 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -27.525kcal/mol
Ligand efficiency (LE) -0.7058kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.324
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 530.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.44
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 88.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 112.28kcal/mol
Minimised FF energy 23.66kcal/mol

SASA & burial

✓ computed
SASA (unbound) 922.0Ų
Total solvent-accessible surface area of free ligand
BSA total 586.3Ų
Buried surface area upon binding
BSA apolar 465.7Ų
Hydrophobic contacts buried
BSA polar 120.6Ų
Polar contacts buried
Fraction buried 63.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2403.9Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 839.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)