FAIRMol

Z49547294

Pose ID 14607 Compound 526 Pose 369

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 Z49547294

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
28.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.52, Jaccard 0.39, H-bond role recall 0.45
Burial
93%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 100% of hydrophobic surface is solvent-exposed (13/13 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 (-1.771 kcal/mol/HA) ✓ Good fit quality (FQ -14.52) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (28.3 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (12) ✗ Internal clashes (8)
Score
-33.655
kcal/mol
LE
-1.771
kcal/mol/HA
Fit Quality
-14.52
FQ (Leeson)
HAC
19
heavy atoms
MW
257
Da
LogP
1.83
cLogP
Strain ΔE
28.3 kcal/mol
SASA buried
93%
Lipo contact
74% BSA apolar/total
SASA unbound
464 Ų
Apolar buried
318 Ų

Interaction summary

HB 13 HY 0 PI 0 CLASH 4 ⚠ Exposure 100%

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

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

HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (13/13 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 13 Buried (contacted) 0 Exposed 13 LogP 1.83 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank1.321Score-33.655
Inter norm-1.613Intra norm-0.159
Top1000noExcludedno
Contacts18H-bonds13
Artifact reasongeometry warning; 8 clashes; 12 protein contact clashes; moderate strain Δ 28.3
Residues
ALA24 ALA70 ASN41 ASP68 GLN42 GLU73 GLY23 GLY25 GLY47 GLY71 LEU39 LYS26 SER22 SER27 SER28 THR44 THR45 THR69

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 overlap11Native recall0.52
Jaccard0.39RMSD-
HB strict5Strict recall0.33
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
369 1.3211693351812412 -1.61277 -33.6549 13 18 11 0.52 0.45 - no Current
463 2.9761509459890605 -1.36448 -26.1784 7 15 0 0.00 0.00 - no Open
415 3.3542602531630394 -1.46927 -30.388 8 10 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 -33.655kcal/mol
Ligand efficiency (LE) -1.7713kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.519
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 257.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.83
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 89.03kcal/mol
Minimised FF energy 60.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 464.5Ų
Total solvent-accessible surface area of free ligand
BSA total 431.5Ų
Buried surface area upon binding
BSA apolar 317.7Ų
Hydrophobic contacts buried
BSA polar 113.8Ų
Polar contacts buried
Fraction buried 92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1214.0Ų
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 503.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)