FAIRMol

ulfkktlib_2489

Pose ID 14421 Compound 1165 Pose 183

DB fairmolDocking 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_2489

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
27.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.57, Jaccard 0.44, H-bond role recall 0.45
Burial
76%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 79% of hydrophobic surface is solvent-exposed (22/28 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.831 kcal/mol/HA) ✓ Good fit quality (FQ -8.39) ✓ Good H-bonds (5 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ High strain energy (27.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (22)
Score
-29.101
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-8.39
FQ (Leeson)
HAC
35
heavy atoms
MW
463
Da
LogP
4.98
cLogP
Final rank
4.9798
rank score
Inter norm
-0.879
normalised
Contacts
18
H-bonds 12
Strain ΔE
27.9 kcal/mol
SASA buried
76%
Lipo contact
69% BSA apolar/total
SASA unbound
706 Ų
Apolar buried
367 Ų

Interaction summary

HBA 5 HY 2 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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: strict.
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 overlap12Native recall0.57
Jaccard0.44RMSD-
HB strict7Strict recall0.47
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

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
248 1.69338793475606 -0.823205 -29.2528 1 18 0 0.00 0.00 - no Open
188 3.395984473509757 -0.879151 -30.5603 7 12 0 0.00 0.00 - no Open
183 4.97979899170821 -0.878582 -29.1007 12 18 12 0.57 0.45 - no Current
233 5.399867504176738 -1.0007 -35.308 7 24 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 -29.101kcal/mol
Ligand efficiency (LE) -0.8314kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.386
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 463.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.98
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 125.37kcal/mol
Minimised FF energy 97.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 706.1Ų
Total solvent-accessible surface area of free ligand
BSA total 534.1Ų
Buried surface area upon binding
BSA apolar 367.2Ų
Hydrophobic contacts buried
BSA polar 166.9Ų
Polar contacts buried
Fraction buried 75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1350.8Ų
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 548.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)