Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
23.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.90, Jaccard 0.86, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.511 kcal/mol/HA)
✓ Good fit quality (FQ -13.12)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (23.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-33.245
kcal/mol
LE
-1.511
kcal/mol/HA
Fit Quality
-13.12
FQ (Leeson)
HAC
22
heavy atoms
MW
344
Da
LogP
0.95
cLogP
Final rank
3.4621
rank score
Inter norm
-1.554
normalised
Contacts
20
H-bonds 8
Interaction summary
HBD 1
HBA 5
HY 2
PI 1
CLASH 1
Interaction summary
HBD 1
HBA 5
HY 2
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 19 | Native recall | 0.90 |
| Jaccard | 0.86 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU: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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 591 | 2.5391141885619666 | -1.12169 | -24.8686 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 568 | 2.805370864558984 | -1.36184 | -28.2203 | 12 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 584 | 3.4621021031939097 | -1.55417 | -33.2451 | 8 | 20 | 19 | 0.90 | 0.36 | - | no | Current |
| 572 | 4.314204209146781 | -1.18549 | -24.4621 | 14 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-33.245kcal/mol
Ligand efficiency (LE)
-1.5111kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.120
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.95
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-148.38kcal/mol
Minimised FF energy
-171.75kcal/mol
SASA & burial
✓ computed
SASA (unbound)
560.1Ų
Total solvent-accessible surface area of free ligand
BSA total
484.5Ų
Buried surface area upon binding
BSA apolar
344.5Ų
Hydrophobic contacts buried
BSA polar
140.0Ų
Polar contacts buried
Fraction buried
86.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1249.0Ų
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
506.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)