FAIRMol

Z25218329

Pose ID 14661 Compound 3553 Pose 423

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 Z25218329

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 strong SASA done
Strain ΔE
41.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.45
Burial
79%
Hydrophobic fit
78%
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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.640 kcal/mol/HA) ✓ Good fit quality (FQ -6.11) ✓ Strong H-bond network (15 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (41.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-18.565
kcal/mol
LE
-0.640
kcal/mol/HA
Fit Quality
-6.11
FQ (Leeson)
HAC
29
heavy atoms
MW
395
Da
LogP
3.55
cLogP
Strain ΔE
41.2 kcal/mol
SASA buried
79%
Lipo contact
78% BSA apolar/total
SASA unbound
698 Ų
Apolar buried
430 Ų

Interaction summary

HB 15 HY 6 PI 1 CLASH 3 ⚠ Exposure 45%
⚠️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 3.55 H-bonds 15
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank3.128Score-18.565
Inter norm-1.079Intra norm0.438
Top1000noExcludedno
Contacts19H-bonds15
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; high strain Δ 41.2
Residues
ALA24 ALA40 ASN126 ASN41 GLU21 GLU73 GLY23 GLY25 GLY71 LEU130 LYS127 LYS159 LYS26 PHE38 SER22 SER27 SER28 THR44 THR69

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

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
Jaccard0.67RMSD-
HB strict6Strict recall0.40
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
428 1.4581929351472553 -0.778672 -20.1406 6 15 0 0.00 0.00 - no Open
423 3.1279449951587117 -1.07852 -18.5653 15 19 16 0.76 0.45 - no Current
399 4.6887857934889245 -0.892793 -14.5107 11 16 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 -18.565kcal/mol
Ligand efficiency (LE) -0.6402kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.111
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.55
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 118.16kcal/mol
Minimised FF energy 76.98kcal/mol

SASA & burial

✓ computed
SASA (unbound) 698.3Ų
Total solvent-accessible surface area of free ligand
BSA total 551.5Ų
Buried surface area upon binding
BSA apolar 429.6Ų
Hydrophobic contacts buried
BSA polar 121.9Ų
Polar contacts buried
Fraction buried 79.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1408.7Ų
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 513.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)