FAIRMol

Z49565795

Pose ID 14906 Compound 563 Pose 668

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 Z49565795

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
12.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.62, H-bond role recall 0.27
Burial
92%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 45% of hydrophobic surface appears solvent-exposed (10/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.155 kcal/mol/HA) ✓ Good fit quality (FQ -10.78) ✓ Good H-bonds (5 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (12.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-31.196
kcal/mol
LE
-1.155
kcal/mol/HA
Fit Quality
-10.78
FQ (Leeson)
HAC
27
heavy atoms
MW
355
Da
LogP
3.37
cLogP
Strain ΔE
12.7 kcal/mol
SASA buried
92%
Lipo contact
84% BSA apolar/total
SASA unbound
620 Ų
Apolar buried
482 Ų

Interaction summary

HB 5 HY 10 PI 1 CLASH 3 ⚠ Exposure 45%

HB · H-bonds
Mode: strict. 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
⚠️Partial hydrophobic solvent exposure
45% of hydrophobic surface appears solvent-exposed (10/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22 Buried (contacted) 12 Exposed 10 LogP 3.37 H-bonds 5
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank2.220Score-31.196
Inter norm-1.133Intra norm-0.022
Top1000noExcludedno
Contacts21H-bonds5
Artifact reasongeometry warning; 12 clashes; 1 protein clash
Residues
ALA158 ALA24 ALA40 ALA70 ASN126 ASN41 ASP68 GLN42 GLU73 GLY23 GLY25 GLY71 LEU39 LYS127 LYS159 LYS26 PHE38 SER27 SER28 THR44 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 overlap16Native recall0.76
Jaccard0.62RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue3HB residue recall0.27

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
668 2.219769786585919 -1.13327 -31.1956 5 21 16 0.76 0.27 - no Current
649 3.083294048470608 -1.01992 -27.9507 6 17 0 0.00 0.00 - no Open
635 3.324688483197734 -0.985934 -26.0878 2 14 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 -31.196kcal/mol
Ligand efficiency (LE) -1.1554kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.779
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.37
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 126.03kcal/mol
Minimised FF energy 113.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 619.7Ų
Total solvent-accessible surface area of free ligand
BSA total 570.7Ų
Buried surface area upon binding
BSA apolar 482.2Ų
Hydrophobic contacts buried
BSA polar 88.5Ų
Polar contacts buried
Fraction buried 92.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1393.7Ų
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 504.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)