FAIRMol

Z25103234

Pose ID 14736 Compound 1812 Pose 498

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 Z25103234

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
6.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.61, H-bond role recall 0.36
Burial
91%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (5/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.7 kcal/mol) ✓ Excellent LE (-1.460 kcal/mol/HA) ✓ Good fit quality (FQ -12.21) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-29.193
kcal/mol
LE
-1.460
kcal/mol/HA
Fit Quality
-12.21
FQ (Leeson)
HAC
20
heavy atoms
MW
308
Da
LogP
2.59
cLogP
Strain ΔE
6.7 kcal/mol
SASA buried
91%
Lipo contact
65% BSA apolar/total
SASA unbound
521 Ų
Apolar buried
307 Ų

Interaction summary

HB 8 HY 3 PI 1 CLASH 4 ⚠ Exposure 38%

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
38% of hydrophobic surface appears solvent-exposed (5/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13 Buried (contacted) 8 Exposed 5 LogP 2.59 H-bonds 8
Exposed fragments: phenyl (2/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.802Score-29.193
Inter norm-1.501Intra norm0.041
Top1000noExcludedno
Contacts16H-bonds8
Artifact reasongeometry warning; 6 clashes; 3 protein clashes
Residues
ALA158 ALA24 ASN126 ASP129 ASP68 GLU73 GLY23 GLY25 LYS127 LYS159 LYS26 PHE38 SER157 SER27 SER28 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 overlap14Native recall0.67
Jaccard0.61RMSD-
HB strict6Strict recall0.40
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

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
496 1.4675456386820787 -1.46578 -27.7263 2 9 0 0.00 0.00 - no Open
489 2.387320273110485 -1.23679 -20.4771 9 14 0 0.00 0.00 - no Open
498 3.801559317682317 -1.50051 -29.1926 8 16 14 0.67 0.36 - 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 -29.193kcal/mol
Ligand efficiency (LE) -1.4596kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.214
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 308.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.59
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 6.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.87kcal/mol
Minimised FF energy 53.17kcal/mol

SASA & burial

✓ computed
SASA (unbound) 521.2Ų
Total solvent-accessible surface area of free ligand
BSA total 473.7Ų
Buried surface area upon binding
BSA apolar 306.9Ų
Hydrophobic contacts buried
BSA polar 166.8Ų
Polar contacts buried
Fraction buried 90.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1212.6Ų
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 493.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)