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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
41.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.39, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
55% of hydrophobic surface appears solvent-exposed (11/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.995 kcal/mol/HA)
✓ Good fit quality (FQ -9.39)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Extreme strain energy (41.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-27.862
kcal/mol
LE
-0.995
kcal/mol/HA
Fit Quality
-9.39
FQ (Leeson)
HAC
28
heavy atoms
MW
374
Da
LogP
3.28
cLogP
Interaction summary
HB 7
HY 12
PI 0
CLASH 1
⚠ Exposure 55%
Interaction summary
HB 7
HY 12
PI 0
CLASH 1
⚠ Exposure 55%
Partial hydrophobic solvent exposure
55% of hydrophobic surface appears solvent-exposed (11/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 9
Exposed 11
LogP 3.28
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (2/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.477 | Score | -27.862 |
|---|---|---|---|
| Inter norm | -1.114 | Intra norm | 0.119 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 7 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; high strain Δ 41.4 | ||
| Residues |
ALA40
ALA48
ASN41
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
LEU31
LEU39
LEU51
LYS26
SER22
SER27
SER28
THR44
| ||
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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 11 | Native recall | 0.52 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 426 | 0.20770404577612916 | -1.13873 | -25.8264 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 1.6818039381286587 | -1.20032 | -26.424 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 455 | 2.477135703355753 | -1.11435 | -27.8624 | 7 | 18 | 11 | 0.52 | 0.36 | - | no | Current |
| 455 | 2.8965566461410885 | -0.813135 | -21.8999 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 3.27287170032687 | -0.914601 | -22.4375 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 3.374781699121479 | -1.05774 | -25.0914 | 8 | 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
-27.862kcal/mol
Ligand efficiency (LE)
-0.9951kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.394
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
374.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.28
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
119.45kcal/mol
Minimised FF energy
78.01kcal/mol
SASA & burial
✓ computed
SASA (unbound)
602.5Ų
Total solvent-accessible surface area of free ligand
BSA total
541.6Ų
Buried surface area upon binding
BSA apolar
432.6Ų
Hydrophobic contacts buried
BSA polar
109.0Ų
Polar contacts buried
Fraction buried
89.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1364.9Ų
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
496.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)