FAIRMol

ulfkktlib_3457

Pose ID 14424 Compound 5240 Pose 186

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
T22
L. donovani rab5a L. donovani
Ligand ulfkktlib_3457

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
19.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.86, Jaccard 0.69, H-bond role recall 0.55
Burial
92%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 93% of hydrophobic surface is solvent-exposed (13/14 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 ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.397 kcal/mol/HA) ✓ Good fit quality (FQ -12.33) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Moderate strain (19.3 kcal/mol) ✗ Geometry warnings
Score
-32.138
kcal/mol
LE
-1.397
kcal/mol/HA
Fit Quality
-12.33
FQ (Leeson)
HAC
23
heavy atoms
MW
341
Da
LogP
-1.28
cLogP
Final rank
3.5993
rank score
Inter norm
-1.509
normalised
Contacts
23
H-bonds 11
Strain ΔE
19.3 kcal/mol
SASA buried
92%
Lipo contact
73% BSA apolar/total
SASA unbound
596 Ų
Apolar buried
400 Ų

Interaction summary

HBD 2 HBA 5 HY 1 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap18Native recall0.86
Jaccard0.69RMSD-
HB strict7Strict recall0.47
HB same residue+role6HB role recall0.55
HB same residue6HB residue recall0.55

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
249 2.869771837438816 -0.836852 -19.1319 6 10 0 0.00 0.00 - no Open
186 3.5992766970661445 -1.50904 -32.1376 11 23 18 0.86 0.55 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -32.138kcal/mol
Ligand efficiency (LE) -1.3973kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.332
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.28
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -46.08kcal/mol
Minimised FF energy -65.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 595.8Ų
Total solvent-accessible surface area of free ligand
BSA total 550.6Ų
Buried surface area upon binding
BSA apolar 400.2Ų
Hydrophobic contacts buried
BSA polar 150.5Ų
Polar contacts buried
Fraction buried 92.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1302.0Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 494.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)