FAIRMol

RAB5A

Pose ID 14918 Compound 5571

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 RAB5A

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 weak Geometry low Native strong SASA done
Strain ΔE
121.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 1.00
Burial
89%
Hydrophobic fit
35%
Reason: 1 severe internal clashes, strain 121.3 kcal/mol
strain ΔE 121.3 kcal/mol 1 severe internal clashes 2 protein-contact clashes 60% of hydrophobic surface is solvent-exposed (6/10 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.
✓ Strong H-bond network (16 bonds) ✓ Deep burial (89% SASA buried) ✗ Extreme strain energy (121.3 kcal/mol)
HAC
28
heavy atoms
MW
440
Da
LogP
-4.35
cLogP
Strain ΔE
121.3 kcal/mol
SASA buried
89%
Lipo contact
35% BSA apolar/total
SASA unbound
597 Ų
Apolar buried
186 Ų

Interaction summary

HB 16 HY 3 PI 1 CLASH 2 Severe 1 ⚠ Exposure 60%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (6/10 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 10 Buried (contacted) 4 Exposed 6 LogP -4.35 H-bonds 16
Exposed fragments: aromatic ring (3/5 atoms exposed)aromatic ring (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank-Score-
Inter norm-Intra norm-
Top1000noExcludedno
Contacts21H-bonds16
Artifact reasonNative reference ligand
Residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28

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 overlap21Native recall1.00
Jaccard1.00RMSD0.00 Å
HB strict15Strict recall1.00
HB same residue+role11HB role recall1.00
HB same residue11HB residue recall1.00

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
- ★ Native - - - 16 21 21 1.00 1.00 0.00 Å no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Heavy atom count 28HA

Physicochemical properties
Molecular weight 440.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -4.35
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 121.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 70.27kcal/mol
Minimised FF energy -51.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 597.2Ų
Total solvent-accessible surface area of free ligand
BSA total 530.9Ų
Buried surface area upon binding
BSA apolar 185.9Ų
Hydrophobic contacts buried
BSA polar 344.9Ų
Polar contacts buried
Fraction buried 88.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 35.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1102.4Ų
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 492.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)